diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index 755309c6fff858e0aa9f5e6e60c512359c9e173f..ae7a4e03f83fe56a6e1a3d05735abc17ca35576f 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -72,7 +72,6 @@ endif()
################################ CMAKE OPTIONS ##################################
-option(WITH_DOC "Build documentation using python-sphinx and doxygen" OFF)
option(VERBOSITY "Set MOOSE verbosity level (deprecated)" 0)
## Unit testing and debug mode.
option(DEBUG "Build with debug support" OFF)
@@ -201,10 +200,6 @@ if(LIBSBML_FOUND)
find_package(LibXML2 REQUIRED)
endif()
include_directories(${LibXML2_INCLUDE_DIRS})
- if(${LIBSBML_LIBRARY_DIRS})
- target_link_libraries(libmoose PROPERTIES LINK_FLAGS "-L${LIBSBML_LIBRARY_DIRS}")
- endif()
-
else()
message(
"======================================================================\n"
@@ -267,23 +262,17 @@ if(WITH_GSL)
# top level.
include_directories( ${GSL_INCLUDE_DIRS} )
elseif(WITH_BOOST)
- find_package(Boost 1.44 COMPONENTS filesystem REQUIRED)
+ find_package(Boost 1.44 COMPONENTS filesystem random REQUIRED)
find_package( LAPACK REQUIRED )
add_definitions( -DUSE_BOOST -UUSE_GSL )
include_directories( ${Boost_INCLUDE_DIRS} )
- # check_include_file_cxx(
- # ${Boost_INCLUDE_DIRS}/boost/random/random_device.hpp
- # BOOST_RANDOM_DEVICE_EXISTS
- # )
- # if(BOOST_RANDOM_DEVICE_EXISTS)
- # add_definitions(-DBOOST_RANDOM_DEVICE_EXISTS)
- # endif(BOOST_RANDOM_DEVICE_EXISTS)
- # check_include_file_cxx(
- # ${Boost_INCLUDE_DIRS}/boost/filesystem.hpp BOOST_FILESYSTEM_EXISTS
- # )
- # if(BOOST_FILESYSTEM_EXISTS)
- # add_definitions( -DBOOST_FILESYSTEM_EXISTS )
- # endif(BOOST_FILESYSTEM_EXISTS)
+ check_include_file_cxx(
+ ${Boost_INCLUDE_DIRS}/boost/random/random_device.hpp
+ BOOST_RANDOM_DEVICE_EXISTS
+ )
+ if(BOOST_RANDOM_DEVICE_EXISTS)
+ add_definitions(-DBOOST_RANDOM_DEVICE_EXISTS)
+ endif(BOOST_RANDOM_DEVICE_EXISTS)
endif()
## Setup hdf5
@@ -513,42 +502,14 @@ if(CMAKE_VERSION VERSION_LESS "2.8.0")
target_link_libraries(moose.bin PUBLIC moose)
ELSE()
target_link_libraries(moose.bin LINK_PUBLIC moose)
- if(LIBSBML_FOUND)
- target_link_libraries(moose.bin LINK_PUBLIC ${LIBSBML_LIBRARIES})
- endif(LIBSBML_FOUND)
ENDIF()
-if(WITH_DOC)
- FIND_PACKAGE(Doxygen REQUIRED)
- add_custom_command(TARGET libmoose POST_BUILD
- COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.full
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
- COMMENT "Building developer documentation"
- VERBATIM
- )
-endif(WITH_DOC)
-
######################### BUILD PYMOOSE ########################################
# Root of all python module.
if(WITH_PYTHON)
add_subdirectory( pymoose )
endif(WITH_PYTHON)
-## Moose documentation
-option(WITH_DOC "Build documentation using python-sphinx and doxygen" OFF)
-if(WITH_DOC)
- FIND_PACKAGE(Sphinx REQUIRED)
- message(STATUS "Build documentation.")
- set(USER_DOC_OUTPUT_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Docs/user/py/_build/html)
- set(DEVELOPER_DOC_OUTPUT_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Docs/developer/html)
- ADD_CUSTOM_TARGET(docs ALL
- COMMAND ./docgen
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
- COMMENT "Generating html doc using sphinx and doxygen"
- )
-
-endif(WITH_DOC)
-
######################### INSTALL ##############################################
install(TARGETS moose.bin
@@ -575,17 +536,6 @@ if(WITH_PYTHON)
endif(WITH_PYTHON)
-if(WITH_DOC)
- message(STATUS "Installing moose doc")
- install(DIRECTORY ${USER_DOC_OUTPUT_DIR}
- DESTINATION share/doc/moose
- )
-
- install(DIRECTORY ${DEVELOPER_DOC_OUTPUT_DIR}
- DESTINATION share/doc/moose/developer
- )
-endif()
-
# Print message to start build process
if(${CMAKE_BUILD_TOOL} MATCHES "make")
message(
diff --git a/moose-core/CheckCXXCompiler.cmake b/moose-core/CheckCXXCompiler.cmake
index dcab851bdd86bef0790a3cd58e183a4f28107e79..7fddd1d2a2e27ccde9e15c778772758977e23b99 100644
--- a/moose-core/CheckCXXCompiler.cmake
+++ b/moose-core/CheckCXXCompiler.cmake
@@ -5,6 +5,8 @@ CHECK_CXX_COMPILER_FLAG( "-std=c++11" COMPILER_SUPPORTS_CXX11 )
CHECK_CXX_COMPILER_FLAG( "-std=c++0x" COMPILER_SUPPORTS_CXX0X )
CHECK_CXX_COMPILER_FLAG( "-Wno-strict-aliasing" COMPILER_WARNS_STRICT_ALIASING )
+
+
# Turn warning to error: Not all of the options may be supported on all
# versions of compilers. be careful here.
add_definitions(-Wall
@@ -18,6 +20,13 @@ if(COMPILER_WARNS_STRICT_ALIASING)
add_definitions( -Wno-strict-aliasing )
endif(COMPILER_WARNS_STRICT_ALIASING)
+# Disable some harmless warnings.
+CHECK_CXX_COMPILER_FLAG( "-Wno-unused-but-set-variable"
+ COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN
+ )
+if(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)
+ add_definitions( "-Wno-unused-but-set-variable" )
+endif(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)
if(COMPILER_SUPPORTS_CXX11)
message(STATUS "Your compiler supports c++11 features. Enabling it")
diff --git a/moose-core/CheckMooseCompiler.cmake b/moose-core/CheckMooseCompiler.cmake
deleted file mode 100644
index dcab851bdd86bef0790a3cd58e183a4f28107e79..0000000000000000000000000000000000000000
--- a/moose-core/CheckMooseCompiler.cmake
+++ /dev/null
@@ -1,36 +0,0 @@
-########################### COMPILER MACROS #####################################
-
-include(CheckCXXCompilerFlag)
-CHECK_CXX_COMPILER_FLAG( "-std=c++11" COMPILER_SUPPORTS_CXX11 )
-CHECK_CXX_COMPILER_FLAG( "-std=c++0x" COMPILER_SUPPORTS_CXX0X )
-CHECK_CXX_COMPILER_FLAG( "-Wno-strict-aliasing" COMPILER_WARNS_STRICT_ALIASING )
-
-# Turn warning to error: Not all of the options may be supported on all
-# versions of compilers. be careful here.
-add_definitions(-Wall
- #-Wno-return-type-c-linkage
- -Wno-unused-variable
- -Wno-unused-function
- #-Wno-unused-private-field
- )
-add_definitions(-fPIC)
-if(COMPILER_WARNS_STRICT_ALIASING)
- add_definitions( -Wno-strict-aliasing )
-endif(COMPILER_WARNS_STRICT_ALIASING)
-
-
-if(COMPILER_SUPPORTS_CXX11)
- message(STATUS "Your compiler supports c++11 features. Enabling it")
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
- add_definitions( -DENABLE_CPP11 )
-elseif(COMPILER_SUPPORTS_CXX0X)
- message(STATUS "Your compiler supports c++0x features. Enabling it")
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
- add_definitions( -DENABLE_CXX11 )
- add_definitions( -DBOOST_NO_CXX11_SCOPED_ENUMS -DBOOST_NO_SCOPED_ENUMS )
-else()
- add_definitions( -DBOOST_NO_CXX11_SCOPED_ENUMS -DBOOST_NO_SCOPED_ENUMS )
- message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++11 support.")
-endif()
-
-
diff --git a/moose-core/Docs/README.txt b/moose-core/Docs/README.txt
deleted file mode 100644
index fe53486074142520a29bcbd8585217a63a57e60d..0000000000000000000000000000000000000000
--- a/moose-core/Docs/README.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-This is the MOOSE documentation directory. The documentation is grouped into
-the following directories:
-
- - user: This is for anyone wishing to learn/use MOOSE.
- This part of the documentation is encoded in Markdown format.
- - developer: If you wish to learn about MOOSE code, go here.
- - doxygen: Source code documentation generation.
- - markdown: This contains a quick introduction to Markdown itself.
- - images: These are images that are included in the user and developer
- documentation.
-
---------------------------------------------------------------------------------
-N.B.: This text file has Windows-style line endings (CR/LF) for easy
-viewing in Windows. We will try to keep the other text files here
-Windows-compatible (e.g.: *.markdown files), but we may slip.
-If you have difficulty viewing them in Notepad, try the inbuilt Wordpad
-editor, or better still, download a good text editor like Notepad++ or Geany.
---------------------------------------------------------------------------------
diff --git a/moose-core/Docs/config/epydoc.cfg b/moose-core/Docs/config/epydoc.cfg
deleted file mode 100644
index 4bd20f4be023fbd94572e859edf48896c4ef3761..0000000000000000000000000000000000000000
--- a/moose-core/Docs/config/epydoc.cfg
+++ /dev/null
@@ -1,152 +0,0 @@
-[epydoc] # Epydoc section marker (required by ConfigParser)
-
-# The list of objects to document. Objects can be named using
-# dotted names, module filenames, or package directory names.
-# Alases for this option include "objects" and "values".
-modules: python/libmumbl
- , python/moose
- , python/rdesigneur
- , gui
-
-# The type of output that should be generated. Should be one
-# of: html, text, latex, dvi, ps, pdf.
-output: html
-
-# The path to the output directory. May be relative or absolute.
-#target: Docs/developer/epydoc
-target: docs
-
-# An integer indicating how verbose epydoc should be. The default
-# value is 0; negative values will supress warnings and errors;
-# positive values will give more verbose output.
-verbosity: 10
-
-# A boolean value indicating that Epydoc should show a traceback
-# in case of unexpected error. By default don't show tracebacks
-debug: 1
-
-# If True, don't try to use colors or cursor control when doing
-# textual output. The default False assumes a rich text prompt
-simple-term: 0
-
-
-### Generation options
-
-# The default markup language for docstrings, for modules that do
-# not define __docformat__. Defaults to epytext.
-docformat: epytext
-
-# Whether or not parsing should be used to examine objects.
-parse: yes
-
-# Whether or not introspection should be used to examine objects.
-introspect: yes
-
-# Don't examine in any way the modules whose dotted name match this
-# regular expression pattern.
-#exclude
-
-# Don't perform introspection on the modules whose dotted name match this
-# regular expression pattern.
-#exclude-introspect
-
-# Don't perform parsing on the modules whose dotted name match this
-# regular expression pattern.
-#exclude-parse
-
-# The format for showing inheritance objects.
-# It should be one of: 'grouped', 'listed', 'included'.
-inheritance: listed
-
-# Whether or not to include private variables. (Even if included,
-# private variables will be hidden by default.)
-private: yes
-
-# Whether or not to list each module's imports.
-imports: yes
-
-# Whether or not to include syntax highlighted source code in
-# the output (HTML only).
-sourcecode: yes
-
-# Whether or not to include a page with Epydoc log, containing
-# effective option at the time of generation and the reported logs.
-include-log: no
-
-
-### Output options
-
-# The documented project's name.
-name: PyMOOSE
-
-# The CSS stylesheet for HTML output. Can be the name of a builtin
-# stylesheet, or the name of a file.
-css: white
-
-# The documented project's URL.
-#url: http://some.project/
-
-# HTML code for the project link in the navigation bar. If left
-# unspecified, the project link will be generated based on the
-# project's name and URL.
-link: <a href="somewhere">PyMOOSE Documentation</a>
-
-# The "top" page for the documentation. Can be a URL, the name
-# of a module or class, or one of the special names "trees.html",
-# "indices.html", or "help.html"
-#top: os.path
-
-# An alternative help file. The named file should contain the
-# body of an HTML file; navigation bars will be added to it.
-#help: my_helpfile.html
-
-# Whether or not to include a frames-based table of contents.
-frames: yes
-
-# Whether each class should be listed in its own section when
-# generating LaTeX or PDF output.
-separate-classes: no
-
-
-### API linking options
-
-# Define a new API document. A new interpreted text role
-# will be created
-#external-api: epydoc
-
-# Use the records in this file to resolve objects in the API named NAME.
-#external-api-file: epydoc:api-objects.txt
-
-# Use this URL prefix to configure the string returned for external API.
-#external-api-root: epydoc:http://epydoc.sourceforge.net/api
-
-
-### Graph options
-
-# The list of graph types that should be automatically included
-# in the output. Graphs are generated using the Graphviz "dot"
-# executable. Graph types include: "classtree", "callgraph",
-# "umlclasstree". Use "all" to include all graph types
-graph: all
-
-# The path to the Graphviz "dot" executable, used to generate
-# graphs.
-# dotpath: /usr/local/bin/dot
-
-# The name of one or more pstat files (generated by the profile
-# or hotshot module). These are used to generate call graphs.
-pstat: profile.out
-
-# Specify the font used to generate Graphviz graphs.
-# (e.g., helvetica or times).
-graph-font: Helvetica
-
-# Specify the font size used to generate Graphviz graphs.
-graph-font-size: 10
-
-
-### Return value options
-
-# The condition upon which Epydoc should exit with a non-zero
-# exit status. Possible values are error, warning, docstring_warning
-#fail-on: error
diff --git a/moose-core/Docs/developer/API.txt b/moose-core/Docs/developer/API.txt
deleted file mode 100644
index 5dddd83a88546f2fb47dd02e26b0ca0a3050bd1f..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/API.txt
+++ /dev/null
@@ -1,215 +0,0 @@
-API for Python interface.
-
-1. Key data structures, not accessed directly, but important for concepts:
- - Element: Managers for objects. This includes data, messaging,
- field info and class info. All Elements can be arrays.
- - Finfo: Field information specifiers, used to build up the MOOSE
- interface to the underlying C++ class. Similar to the old MOOSE.
- Major Subclasses:
- - DestFinfo: used for functions of the Object. Can be called
- either using SetGet::set or by messages.
- - SrcFinfo: Used to call messages.
- - ValueFinfo: Used to define fields. The ReadOnly kind has
- just the 'get' function, whereas the normal kind
- also has a 'set' function. Both 'get' and 'set' are
- implemented as DestFinfos.
- - Cinfo: Class information specifier, used to specify class name,
- inheritance, and manage the array of Finfos.
- - Msg: Messages. Many subclasses. Handle communication between Elements.
- All Msgs are between precisely two Elements. So the Elements are nodes
- and the Msgs are edges. Msg have a lot of variety in how they control
- data transfer between individual array entries within the source and
- destination Element. Data transfer can be bidirectional.
- All Msgs provide a handle to an Element called a MsgManager, which
- allows you to inspect the Msg fields and in some cases modify them.
- But you cannot modify the source and destination Elements.
-
-2. Key data structures that you will access.
-
-Id: Handle to Elements.
-DataId: Handle to objects on Elements. Has a data part and a field part.
- The data part is the parent object, and is used for any array Element.
- The field part is for array fields within individual data entries,
- in cases where the array fields themselves are accessed like Elements.
- For example, in an IntFire neuron, you could have an
- array of a million IntFire neurons on Element A, and each IntFire
- neuron might have a random individual number, say, 10000, 15000, 8000,
- etc Synapses. To index Synapse 234 on IntFire 999999 you would use a
- DataId( 999999, 234).
-
-ObjId: Composite of Id and DataId. Allows you to uniquely identify any entity
- in the simulation.
-
-
-3. Field assignments and function calls:
- File: SetGet.h
- This has a series of templates for different argument cases.
- 1. If you want to call a function foo( int A, double B ) on
- ObjId oid, you would do:
-
- SetGet2< int, double >::set( oid, "foo", A, B );
-
- 2. To call a function bar( int A, double B, string C ) on oid:
- SetGet3< int, double, string >::set( oid, "bar", A, B, C );
-
- 3. To assign a field value "short abc" on object oid:
- Field< short >::set( oid, "abc", 123 );
-
- 4. To get a field value "double pqr" on object obj:
- double x = Field< short >::get( oid, "pqr" );
-
- 5. To assign the double 'xcoord' field on all the objects on
- element Id id, which has an array of the objects:
- vector< double > newXcoord;
- // Fill up the vector here.
- Field< double >::setVec( id, "xcoord", newXcoord );
- Note that the dimensions of newXcoord should match those of
- the target element.
-
- You can also use a similar call if it is just a function on id:
- SetGet1< double >::setVec( id, "xcoord_func", newXcoord );
-
- 6. To extract the double vector 'ycoord' field from all the
- objects on id:
- vector< double > oldYcoord; // Do not need to allocate.
- Field< double >::getVec( id, "ycoord", oldYcoord );
-
- 7. To set/get LookupFields, that is fields which have an index
- to lookup:
- double x = LookupField< unsigned int, double >::get( objId, field, index );
- LookupField< unsigned int, double >::set( objId, field, index, value );
-
- There are lots of other variants here.
-
-4. Shell commands to use: the ones that start with 'do'.
-
-Id doCreate( string type, Id parent, string name,
- vector< unsigned int > dimensions );
-
-bool doDelete( Id id )
-
-MsgId doAddMsg( const string& msgType,
- ObjId src, const string& srcField,
- ObjId dest, const string& destField);
-
-void doQuit();
-
-void doStart( double runtime );
-
-void doNonBlockingStart( double runtime );
-
-void doReinit();
-
-void doStop();
-
-void doTerminate();
-
-void doMove( Id orig, Id newParent );
-
-Id doCopyId orig, Id newParent, string newName,
- unsigned int n, bool copyExtMsgs);
-
-Id doFind( const string& path ) const
-
-void doSetClock( unsigned int tickNum, double dt )
-
-void doUseClock( string path, string field, unsigned int tick );
-
-Id doLoadModel( const string& fname, const string& modelpath );
-
-void doSyncDataHandler( Id elm, const string& sizeField, Id tgt );
-
-
-5. Important fields of important objects.
-
-5.1. Shell object. This is the root object, '/' or '/root'.
-This has the following fields of note:
- - bool isRunning: ReadOnlyValue
- - Id cwe: Regular value.
-
-5.2 Neutral. These fields are shared by all objects.
- string name
- ObjId parent // Parent ObjId. Note this is fully
- // specified, including index.
- vector< Id > children // All child elements.
- string path // Full path
- string className
- unsigned int linearSize // Product of all dimensions
- // Currently not working.
- vector< unsigned int> Dimensions
- unsigned int fieldDimension // Size of field dimension.
- vector< ObjId > msgOut // MsgManagers of all outgoing msgs
- vector< ObjId > msgIn // MsgManagers of all incoming msgs
- vector< Id > msgSrc( string field ) // Ids of source msgs into field
- vector< Id > msgDest( string field ) // Ids of dest msgs into field
-
-5.3 Class Info objects. These are located in /classes/<classname>
- string docs // currently not implemented
- string baseClass // Name of base class
-
-5.4 Field Info objects. These are children of the respective ClassInfo and
- are located in /classes/<classname>/<Field category>
- There are 5 field categories:
- srcFinfo
- destFinfo
- valueFinfo
- lookupFinfo
- sharedFinfo
- Each of these is an array, indexed as DataId( 0, <index> )
- since they are FieldElements.
- You can query the # of entries in each category using
- Id classId( "/classes/<classname>" );
- numValueFinfos =
- Field< unsigned int >::get( classId, "num_valueFinfo" );
-
- Finally each of the field categories has the following fields:
- string name
- string docs // This is implemented
- string type // String with argument types separated by
- // commas. Can handle basic types, Ids,
- // ObjIds, DataIds, strings, and vectors of
- // any of the above.
- vector< string > src // vector of subsidiary srcFinfos, which
- // happens in SharedFinfos.
- vector< string > dest // vector of subsidiary destFinfos, which
- // happens in SharedFinfos and ValueFinfos.
-
-
-
-6. Message traversal, C++ level:
-General approach:
- - If you just want src/dest Id, use the Neutral or Element functions
- to find list of source or target Ids as per spec.
- - Netural::msgSrc( string field );
- - Netural::msgDest( string field );
- - Element::getOutputs( vector< Id >& ret, const SrcFinfo* finfo)
- - Element::getInputs( vector< Id >& ret, const DestFinfo* finfo)
-
- - If you want to iterate through specific array and/or field
- entries in src/dest Id, then you will have to look up the
- MsgIds themselves.
- - vector< ObjId > Neutral::msgOut():
- Not very specific, just the ObjIds of the MsgManagers
- of all outgoing Msgs.
- - vector< ObjId > Neutral::msgIn():
- All ObjIds of MsgManagers of incoming Msgs.
- - MsgId Element::findCaller( FuncId fid ) const:
- Looks up the first Msg that calls the specified Fid
- - Element::getInputMsgs( vector< MsgId >& caller, FuncId fid)
- Fills up vector of MsgIds that call the specified fid
-
- - To convert between MsgIds, Msgs, and the manager ObjId:
- - MsgId Msg::mid(): returns the MsgId of the Msg.
- - Msg::manager(): returns the manager Eref of a Msg.
- - Msg::manager().objId(): returns the manager ObjId of a Msg.
- - static const Msg* Msg::getMsg( MsgId mid )
- Returns the Msg ptr given a MsgId.
-
- - To iterate through Msg targets:
- unsigned int Msg::srcToDestPairs(
- vector< DataId >& src, vector< DataId >& dest) const
- This function gives matching vectors of src and dest
- pairs for the Msg. This should be node-independent,
- but the SparseMsg currently doesn't handle it right,
- and works only on 1 node.
-
diff --git a/moose-core/Docs/developer/BuildingNewMOOSEClasses.txt b/moose-core/Docs/developer/BuildingNewMOOSEClasses.txt
deleted file mode 100644
index a188314665ad515d6115eb1d9b5964e8139e9dbb..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/BuildingNewMOOSEClasses.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-Building new MOOSE classes.
-
-- Take your existing class.
-- Set it up to use access functions of this form:
-
- For things that should look like Read/Write variables to the user:
- void setField( FieldType value );
- FieldType getField() const;
-
- For things that should look like ReadOnly variables to the user:
- FieldType getField() const;
-
- For things that should look like functions to the user:
- ( MOOSE can handle up to 6 arguments )
- void func( Type1 arg1, Type2 arg2 );
-
-- Put in the following function in the header:
- static const Cinfo* initCinfo();
-
-
-- Figure out your MOOSE interface. There are three main kinds of fields,
- which are going to be set up using Finfo objects (short for Field
- Information).
- The three are:
- - DestFinfos: These handle function requests.
- - SrcFinfos: These call functions on other objects. In other
- words, they send messages.
- - ValueFinfos: These support field assignment and readout.
-
-
-- Define initCinfo() in your .cpp, as follows:
-
diff --git a/moose-core/Docs/developer/CodingConventions.txt b/moose-core/Docs/developer/CodingConventions.txt
deleted file mode 100644
index 7e9017608e798f0b688c9f895544a7f1f431ebe3..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/CodingConventions.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-Naming conventions:
-General: Use CamelCase
-Don't use underscores as word separators.
-Classes start with caps
-Fields and functions start with lower case, except for scientific
- conventions (e.g., Vm_) in which case the scientific convention is used.
-Private fields end with an underscore (e.g., Vm_ );
-Use spaces liberally, and always after a comma.
-Field assignment functions (set/get) start with set/get<fieldName>
-
-Naming of MOOSE fields and functions:
-Fields (ValueFinfos): Just use the name of the field, e.g., Vm, x, y, z.
-Message sources (SrcFinfos): Use the name of the field, e.g., output,
- unless there is a name-clash with a Fields. Then use name<Suffix>
- e.g., nOut, xOut, VmOut.
- If the message source is to request a return value, generally use the
- form request<fieldName>
-Message destination (DestFinfos): Use the name of the function, typically a
- verb. e.g., increment, process.
- Special case comes up with the internal set/get functions of fields,
- which are implemented as DestFinfos. Here the DestFinfos are
- automatically named set_<fieldname> and get_<fieldname>
- If the message dest handles a request or other operation as part of
- a shared message, generally use the form
- handle<name>
- If there is an overlap with a SharedMessage or field after applying
- all these rules, then use the form handle<name>.
-Shared messages (SharedFinfos): Use the name of the message.
- If there is an overlap with any other message, the SharedMessage takes
- precedence. This is because Shared Messages are the interface users
- will normally use. Try to avoid overlaps with field names.
-
diff --git a/moose-core/Docs/developer/DesignDocument b/moose-core/Docs/developer/DesignDocument
deleted file mode 100644
index e652b413f921d4c334c91defab2134aabdf1ddab..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/DesignDocument
+++ /dev/null
@@ -1,778 +0,0 @@
-MOOSE redesign for messaging.
-Goals:
-1. Cleanup.
-2. Handle multithreading and MPI from the ground up.
-
-Why do this?
-It is a huge amount of work to refactor a large existing code base. This is
-needed here, and was in fact anticipated, for two reasons:
-- We needed the experience of building a fairly complete, functioning system
- to know what the underlying API must do.
-- The original parallel stuff was a hack.
-
-This redesign does a lot of things differently from the earlier MOOSE messaging.
-- Introduces a buffer-based data transfer mechanism, with a fill/empty
- cycle to replace the earlier function-call mechanism. The fill/empty
- cycle is needed for multithreading and also works better with multinode
- data traffic.
-- All Elements are now assumed to be array Elements, so indexing is built into
- messaging from the ground up.
-- There is a split between synchronous messaging (exact amount of data
- transferred on every timestep) and asynchronous messaging (variable
- amounts of data transferred). This split is at the data transfer
- level but the message specification should be nearly the same.
-- Field access function specification is cleaner.
-- Separation of function specification from messaging. This means that any
- message can be used as a communication line for any function call
- between two Elements. This gives an enormous simplification to message
- design. However, it entails:
-- Runtime type-checking of message data, hopefully in a very efficient way.
- As message setup is itself runtime, and arbitrary functions can sit
- on the message channels, it turns out to be very hard to
- do complete checking at compile or setup time.
-- Wildcard info merged into messages.
-- Three-tier message manipulation hierarchy, for better introspection and
- relating to higher-level setup calls. These are
- Msg: Lowest level, manages info between two Elements e1 and e2.
- Deals with the index-level connectivity for the Element arrays.
- Conn: Mid level. Manages a set of Msgs that together make a messaging
- unit that takes a function call/data from source to a set of
- destination Elements and their array entries. Has introspection
- info. Is a MOOSE field.
- Map: High level. Manages a set of Conns that together handle a
- conceptual group. Equivalent to an anatomical projection from
- one set of neurons to another in the brain. Equivalent to what
- the 'createmap' function would generate. Has introspection.
- Is a MOOSE Element.
-
-- Field access and function calls now go through the messaging interface. Not
- necessarily the fastest way to do it, but simplifies life in a
- multinode/multithreaded system, and reduces the complexity of the
- overall interface.
-
-
-------------------------------------------------------------------------------
-Control flow.
-
-Developer design:
-Every object being scheduled has to provide a 'process' and a 'reinit' function,
-which are set up as a shared message, as per the following interface:
-
-static DestFinfo process(
- "process", "description", new ProcOpFunc< Class>( &Class::process ) );
-static DestFinfo reinit(
- "reinit", "description", new ProcOpFunc< Class>( &Class::reinit ) );
-static Finfo* procShared[] = { &process, &reinit };
-static SharedFinfo( "proc", "description", procShared,
- sizeof( procShared ) / sizeof( const Finfo* ) );
-
-These functions are called specially by the scheduler, and bypass the regular
-message queuing system.
-
-During Reinit, the initial conditions are set and state variables are sent out
-(see below). Reinit happens just at the start of the calculation.
-During Process, first all pending messages are cleared, then internal updates
-happen and data is sent out. Process is repeated once each timestep for each
-Element.
-Process even within the same timestep, can be strictly ordered by clock tick.
-In other words, the messages are handled and the internal updates are done
-within one clock tick, before the next is begun.
-
-Supposing you have two classes A and B. Class A has the state variables of
-the calculation, and class B computes rates of change and sends these back.
-We need to put these on separate clock ticks. When running, this
-is the sequence your classes should follow:
-
-REINIT:
-A reinits and sends out data, typically the state variables.
-
-PROCESS:
-Stage 0:
- B handle msgs
- B send update
-Stage 1:
- A handle msgs
- A send update.
-
-
-
-1. Scheduling.
-Shell::start( double runtime )
- Sets up thread stuff
- Configures clocks for barriers, threads, etc.
- Inits threads with Clock::threadStartFunc
- Clock::threadStartFunc
- Clock::tStart
- Sets up grouping for current thread
- TickPtr::advance
- Tick::advance on all ticks.
- pthread_barrier_wait
- On first thread only: Qinfo::mergeQ
- Puts local data into InQ
- pthread_barrier_wait
- Qinfo::readQ: handle msgs in InQ
- Call process on all scheduled Elements.
- pthread_barrier_wait
- sorts TickPtrs.
- pthread_exit
-join threads
-clean up
-
-
-As before, we have a hierarchy of Shell, Clock, and Tick.
-The Tick now becomes an ArrayField of the Clock. This means that the clock
-can manipulate Ticks directly, which is much easier to understand. However,
-Ticks still look like Elements to the rest of the system and have their
-own messages to all scheduled objects.
-The TickPtr is an intermediate wrapper for Ticks that helps to sort them
-efficiently.
-The Tick object is the one that connects to and calls operations on target
-Elements.
-Ticks call the 'process' function on Elements. This bypasses the queueing
-system, but uses the regular field definition system. There is a somewhat
-specialised OpFunc: ProcOpFunc, which handes type conversions for calls
-emerging from Ticks. This is the sequence:
-Tick::advance
-Iterate over all outgoing Process messages.
- call Msg::process( procinfo, fid )
- call e2->process( procinfo, fid );
- call dataHandler->process( p, elm, fid )
- Get the OpFunc corresponding to fid.
- cast to ProcOpFuncBase, check.
- Scan over the elm array indices
- suitable for current thread.
- call opFunc->proc( obj, eref, p)
- Typecasts obj
- calls obj->process( eref, p )
-
-
-Ticks also call the global Qinfo::readQ() function. This handles all
-asynchronous message passing including spike events and setup calls.
-The old reinit/reset/resched is gone, it will be a function call triggered
-through clearQ.
-
-2. ASYNCHRONOUS MESSAGING
-Async messages work at two levels. First, the developer sees the creation and
-calls to messages within MOOSE objects. Second, the data transfer happens
-under the surface through queues that span threads and nodes.
-
-2.1 Data structures used for messages within MOOSE objects.
-Messages are called through the static const instances of SrcFinfos.
-As described elsewhere, SrcFinfos are initialized along with other Element
-fields at static initialization time.
-SrcFinfo< T1, T2...>( name, description, slot );
- The slot here is a BindIndex, which looks up which Message and Function
- will be called by SrcFinfo::send.
- Slot 0 is reserved for parent->child messages
- Slot 1 is reserved for element->msgSpec messages
- Slots 2 onward are used for data-transfer messages.
- For now each data-transfer slot is predefined.
- Later, if there is a proliferation of costly slot definitions, it
- should be possible to predefine slots only for those SrcFinfos which
- need to be executed efficiently. Other slots will have to generate an
- entry on the fly.
-
-2.1.1 Element-level messaging data structures.
-The Element carries two messaging data structures:
- vector< MsgId > m_; // Handles incoming messages
- vector< vector< MsgFuncBinding > > msgBinding_; // Handles outgoing msgs
-
-The first of these is just to keep track of what comes in to the Element.
-The msgBinding_ is indexed by the slot described above, which is of type
-BindIndex. Each slot refers to a vector of MsgFuncBinding objects, which are
-basically pairs of MsgIds and FuncIds.
-When send executes, the code iterates through this vector of MsgFuncBinding
-objects, adding each MsgId/FuncId pair into the outgoing queue.
-
-2.1.2 Shared messages and messages with many distinct target classes/functions
-There are often cases where a pair of objects must exchange multiple kinds
-of information. When this happens, we want to use a single Msg between the
-two, to keep track of the trajectory of the data, but we want to send
-many kinds of data along this Msg.
- Example 1: when getting a field, the querying object needs to tell
- the responder what information to send, and the responder must send
- back the field value. This is a single Msg, but different kinds of
- data travel in different directions along it in this case.
- To accomplish this, the querying object sets up an entry in its
- msgBinding_ vector. The responding object in this special case
- just puts the other end of the Msg in its m_ vector.
- - Execution works as follows: Querying object calls send< FuncId >
- where the FuncId identifies the 'get_field' function on the responder.
- The get_field function is registered automagically by the Field< T >
- field definition as a GetOpFunc. The operation done by this function
- is to get the field value, and send it right back along the querying
- Msg using somewhat low-level call to Qinfo::addSpecificTargetToQ.
- Example 2. A molecule might send a display object both its xyz
- coordinates, and also its state. It might do so at different times,
- called by different SrcFinfo::send functions.
- Here we have more than one kind of data go from the source
- to the target object.
- - To accomplish this, the two SrcFinfos have distinct slot values,
- pointing to distinct msgBinding_ entries. The MsgFuncBindings point
- to the same MsgId but distinct FuncIds for the respective SrcFinfos.
- Example 3. A molecule sends its conc to a reaction, and the reaction
- sends back the change in conc on each timestep.
- - This is really a sync message problem. If done using async calls,
- the SrcFinfos on either side of the Msg would point to their own
- msg slots, each referring to a BindIndex entry. We don't really worry
- about what the m_ vector does, it isn't too costly for this to
- maintain the Msg at one or both sides of the msg, but it isn't
- necessary either. Since the Shared Msg setup will use a single call,
- it is not hard to do it efficiently. Since the high-level details of
- the Msg are stored in the MsgSpec, we don't worry too much about
- traversal either.
-
-2.2 Calls to messages within MOOSE objects.
-To send a message, one just calls
- srcFinfoInstance->send( Eref current, ProcInfo p, arg1, arg2 ... )
-
-
-Scheduling:
-clearQ: Manages the event queue for the async messaging. Here are the calls:
-
-Tick::advance(): // Calls Qinfo::clearQ on the global event queues.
-Qinfo::clearQ: marches through the queue, each entry of which identifies the
- operative message and hence target Element. Also identifies function
- to call, and the arguments.
-Msg::exec: specialized for each Msg subclass. Calls func on all target entries.
-
-Still to do: Sort out flow control to interface threads such as graphics
-and console. Presumably these would go through other Jobs. There is some
-trickiness in how they fill in queues for the regular objects to clear.
-
-Functioning:
-This is how asynchronous messaging works.
-slot s = Slot1< double >(Conn#, Init<TargetType>Cinfo()->funcInfo("funcName"));
- This slot constructor does an RTTI check on the func type, and if OK,
- loads in the funcIndex. If bad, emits warning and stores a safety
- function.
- Limitation: handling multiple types of targets, whose Functions are
- not just inherited variations. e.g., conc -> plot and xview.
- To get round it: these are simply distinct Connections.
-s->send( Eref e, double arg ); // Uses s to send the data in a typesafe way.
- Converts the funcId and argument into a char buffer.
-void Eref::asend( Slot s, char* arg, unsigned int size);
- //Looks up Conn from Slot, passes it the buffer with funcId and args.
-void Conn::asend( funcIndex, char* arg, unsigned int size);
- // Goes through all Msgs with buffer.
-void Element::addToQ( FuncId funcId, MsgId msgId, const char* arg, unsigned int size );
- Puts MsgId, funcId and data on queue. May select Q based on thread.
- Multi-node Element needs a table to look up for MsgId, pointing to
- off-node targets for that specific MsgId. At this time it also inserts
- data transfer requests to those targets into the postmaster buffers.
- Looks up opFunc, which is also an opportunity to do type checking in
- case lookup shows a problem.
-OpFunc Element::getOpFunc( funcId ); // asks Cinfo for opFunc.
-OpFunc cinfo::getOpFunc( funcId );
-<Need to clear up arguments of functions above>
-At this point all the info is sitting in the asyncQueue of the target Element.
-Eventually the scheduling gets round to calling clearQ as discussed above.
-<Need to put in handling of synaptic input>
-
-
-SYNCHRONOUS MESSAGING
-Scheduling:
-process: Manages synchronous messaging, which is similar to the traditional
- GENESIS messaging in that objects transfer fixed amounts of data every
- timestep. Here are the calls:
-Tick::process(); // Calls Process on targets specified by Conn.
-Conn::process( const ProcInfo* p ); // Calls Process on all Msgs.
-Msg::process( const ProcInfo* p ); // Calls Process on e1.
-Element::process( const ProcInfo* p );// Calls Process on all Data objects.
- Partitions among threads.
-virtual void Data::process( const ProcInfo* p, Eref e );
- Asks e to look up or sum the incoming data buffers, does computation,
- sends out other messages. This involves dumping data directly into
- the target sync buffers. Note that the memory locations are fixed
- ahead of time and are distinct, so this can be done simultaneously
- from multiple threads.
-
-Functioning:
-
-Here are the calls that the Elements/Data use to send out data:
-
-<Here Slot means an index to the hard-coded location for the buffer, different
-from the new Slot class above. Will need to clear up nomenclature.>
-void ssend1< double >( Eref e, Slot s, double arg ); // Calls Eref::send.
-Eref::send1( Slot slot, double arg); // Calls Element::send
-Element::send1( Slot slot, unsigned int eIndex, double arg );
- Puts data into buffer: sendBuf_[ slot + i * numSendSlots_ ] = arg;
-Note that we assume all sync data transfer is doubles. Probably a good
-assumption, may help with data alignment.
-
-Here are some of the calls that Elements use to examine the dumped data:
-double Eref::oneBuf( Slot slot );
- Looks up value in sync buffer at slot:
- return *procBuf_[ procBufRange_[ slot + eIndex * numRecvSlots_ ] ];
-double Eref::sumBuf( Slot slot );
- Sums up series of values in sync buffer at slot. Uses similar operation
- except that it iterates through the offset variable:
- offset = procBufRange_.begin() + slot + i * numRecvSlots_;
-double Eref::prdBuf( Slot slot, double v );
- multiples v into series of values in sync buffer at slot, similar
- fast iteration through buffer using offset.
-
-< To clarify: How to set up these buffers when defining messages >
-
-
-SPORADIC FUNCTION CALLS
-Case 1: Existing message between Elements, using all targets:
-Slot* s = Slot1< double >(...)
-s->send( Eref e, [args] )
-Case 2: Message does not exist
-bool set< double >( Id tgt, FieldId f, double val );
-bool set< double >( Id tgt, const string& fieldname, double val );
-Both of these functions create a temporary object and add a temporary message.
-<More details to come>
-Case 3: Message exists, but want to send to a single target:
-s->sendTo( Eref me, Id tgt, [args] );
-
-=============================================================================
-FIELD ACCESS. Updated 18 Apr 2010.
-Field and function access is routed through the Shell object, /root.
-The Shell is present on all nodes.
-For the coder, the field access functions have a templated front-end described
- below. This is more efficient than the string interface functions.
-For the parser talking to the Shell, the field/func access functions go through
- string-ified arguments void doSet( Id, DataId, field, args) and
- string doGet( Id, DataId, field )
-
-These functions are mediated by the SetGet<N>< Type > class templates.
-N can be any number of arguments, from 0 to 5.
-Each provides one consistent function:
-SetGet1< double >::set( const Eref& dest, const string& field, A arg )
-
-For N = 1 we also have the following functions.
-SetGet1< double >::strSet( const Eref& dest, const string& field,
- const string& val )
-string SetGet1< double >::strGet( const Eref& dest, const string& field )
-SetGet1< double >::setVec( const Eref& dest, const string& field,
- const vector< A >& arg )
-We would like to also make a function:
-SetGet1< double >::getVec( const Eref& dest, const string& field,
- vector< A >& arg )
-
-In addition, the Field< Type > template is derived from SetGet1< A > and
-is designed to interface with the automatically generated functions for
-field access from ValueFinfo: set_<fieldname> and get_<fieldname>
-It provides type-specific functions:
-bool Field< double >::set( const Eref& dest, const string& field, double arg )
-double Field< double >::get( const Eref& dest, const string& field )
-
-
-Inner functioning.
-Set works as follows:
-
-Func Src Dest Args
-Master::innerDispatchSet
- requestSet Worker: handleSet Id, DataId, FuncId,
- Prepacked Buffer
-Worker::handleSet
- lowLevelSet Target::set_field None: hacks in the data.
- ack Master::handleAck
-
- -------------
-Get works as follows.
-
-Func Src Dest Args
-Master::innerDispatchGet
- requestGet Worker::handleGet Id, DataId, FuncId
-
-Worker::handleGet on non_tgt node
- ack Master::handleAck
-Worker::handleGet on tgt node
- lowLevelGet Target::get_field:: Eref, buf
- GetOpFunc
-
-Target::get_field::GetOpFunc::fieldOp
- Hacked func Worker::recvGet node, status,
- to add directly from RetFunc PrepackedBuffer
- into Q
-
-Worker::recvGet
- Puts the data into the buffer
- calls handleAck to complete the operation.
-
-Field access is set up using ValueFinfo and its variants.
-ValueFinfo: uses
- setFunc of form void ( T::*setFunc )( F )
- getFunc of form F ( T::*getFunc )() const
-to access fields. Wraps these functions into OpFunc1 and GetOpFunc. Generates
-functions named "set_" + fieldname and "get_" + fieldname for the Finfo array.
-
-ReadOnlyValueFinfo: Similar, only doesn't use the setFunc.
-
-
-Internals for SetGet access to fields.
-Sets:
-1. DestFinfos provide templated functions with different types and # of args.
- SetGet< ArgTypes >::set( const Eref& dest, const string& field, Args)
- This munges the arguments into a char* array.
-2. Shell::innerSet( Eref, funcId, val, size ) (taking over SetGet::iSetInner)
- This creates a message to the target Eref:Finfo, and passes the data.
- This message is predefined
- - Not deleted/recreated for different targets, just changes
- the target
- - Avoid running up the MsgIds for this Msg. It is always the
- same on all nodes.
- - Avoid having different nodes end up with different MsgIds
- due to creation on local node.
- 2.1 When running on multiple nodes, this first sends out the data
- to all workers and the owner of the target object has to deal with it.
- 2.2 The owner shell then passes back an ack to the master node.
-3. The target function sends back an ack to the calling Shell? Need this to
- ensure serial operation. But it will mess up Destfinfos.
-
-Gets:
-1. ValueFinfos provide the proper combination of a handler and a return
- function that sends the return value back.
- Field< Type > currently handles the return op, not sure why.
- Type Field< Type >::get just passes data on to the Shell::innerGet
-2. Shell::innerGet( Eref, DataId, requestFid, handleFid, field )
- replaces SetGet::iGet in doing field validation, setting up msgs,
- and sending request. Now it polls till the return comes in.
-3. Shell::handleGet deals with the return value, just bunging it into a buffer
- on the Shell object. We don't know yet what the type is.
-4. Shell::innerGet again, having waited till the data came home. Passes
- data back to the Field< Type >::get.
-5. Field< Type >::get now has a buffer and knows how to deal with it, converts
- back to the desired type and returns.
-Note that we can probably replace all of the Field stuff with SetGet1< Type >.
-
-We have a small problem here when handling array fields that also need to
-refer to the parent object. For example, when dt values on clock ticks are
-modified the parent clock needs to do some re-sorting.
-
-A related problems is to set up zombies. In all these cases, things would be
-easier if we always had access to the full DataId as one of the function
-arguments, as in UpFunc. This is untidy for regular function calls.
-For that matter we might want to use yet more information arguments, such
-as the target Element and the Qinfo, as in Epfuncs.
-
-------------------------------------------------------------------------------
-Setup
-FIELD DEFINITION
-Similar to earlier MOOSE, have an initClassInfo function for each class,
-that is meant to be called in order at static initialization. The ordering
-is ensured by having the static initializers call the static initializers
-of their own base classes.
-
-With initClassInfo, set up a static array of finfos. Entries like:
-new Finfo( async1< Reac, double, &Reac::setKf >, "Kf" )
-Function handling is cleaner in at least three ways:
-- It does not require static typecasting of functions,
-- It does static typecasting of the char buffer within a templated function
-- It uses member functions of the Data class directly, rather than static
- functions.
-
-Note that a single Finfo might refer to more than one OpFunc. For example,
-a ValueFinfo will typically define a set func and a get func.
-A LookupFinfo will define a set func with index, a get func with index, a
- get func to return size of table, and a get func to return the whole
- table.
-
-<Still need to fully define how the Finfos control runtime message setup>
-
-ValueFinfo: Stores functions for set and get operations on a specific field.
-LookupFinfo: Stores functions for set with index, get with index, a
- get to return size of table, and a get to return the whole table.
-DestFinfo: Stores a single function.
-SrcFinfo: Defines origin of a message. Manages the send and sendTo operations.
- Typed. Provides index for FuncId lookup.
-Note that the Finfos do NOT map one-to-one to the funcs.
-
-The Finfo may have multiple functions in it. Each function is defined using
-an Ftype that provides 3 functions:
-constructor: Loads in the function of the form &Reac::setKf.
-checkSlot( const Slot* s): Does RTTI check on the slot to ensure compatibility.
-op( Eref e, const char* buf): converts the data entry and buffer and calls func.
-
-MESSAGE SETUP
-bool add( Element* src, const string& srcField,
- Element* dest, const string& destField );
- Decides if fields are for simple or shared messages.
-Case 1: Simple Msg:
-bool addMsgToFunc( Element* src, const Finfo* finfo, Element* dest, FuncId fid )
- Makes a new Msg, with Src and Dest Elements.
-Msg::Msg( src, dest ): constructor registers the new Msg on the src and dest:
- Element::addMsg( m )
- This part needs thought, to decide what kind of Msg to make.
-Conn::add( m): To put the Msg on the Conn.
-src->addConn : To put the conn on the Src.
-src->addTargetFunc: To put the target Func info on the Src.
-
-Case 2: Shared Msg.
-addSharedMsg( Element* src, const Finfo* f1, Element* dest, const Finfo* f2 )
-Yet to implement.
-
-------------------------------------------------------------------------------
-Tree operations.
-Move:
-Shell::doMove( Id orig, Id newParent )
-This function moves the object orig to the new parent NewParent. It does so
-by deleting the old parent->child Msg and creating a new one.
-
-Shell::doCopy( Id orig, Id newParent, string newName, unsigned int n, bool copyExtMsgs)
-This function creates a copy of the 'orig' object and all its descendants.
-It renames the object to 'newName'.
-This copy includes all parameters and state variables. The copy can be multiple,
-so that the single original now becomes an array of size n. If this happens
-then the DataHandlers of the copy have to be upgraded to the next higher
-dimension. Likewise, Messages must also be upgraded.
-The copy always includes the messages that were within the copied tree. If the
-copeExtMsgs field is True then all messages are copied.
-Present status: only n = 1 and copyExtMsgs = 0 are currently supported.
-Tested with all current implementations of messaging.
-Not tested on multiplen nodes.
-
-Shell::doDelete( Id i )
-Destroys Id i, all its messages, and all its children.
-
-------------------------------------------------------------------------------
-OpFunc lookup
-Every function used by MOOSE has a unique FuncId, consistent across nodes.
-This is assigned at static initialization time when the Cinfo constructor
-scans the FinfoArray.
-Managed in Cinfo::funcs_[FuncId]
-Assigned in Cinfo::init using Finfo::registerOpFuncs
-
-There is a static global vector of OpFuncs in the Cinfo class that has entries
-for every function so defined. The FuncId is the index into this vector.
-Additionally, each Cinfo instance has a vector of OpFuncs applicable to itself,
-again indexed by FuncId. Invalid FuncIds for the class have a zero pointer.
-
-FuncId 0 is a dummy function.
-
-------------------------------------------------------------------------------
-Solvers
-Solvers take over operation of a number of regular objects. This is done
-by replacing the data and class info of the original, with special
-'Zombie' versions provided by the solver. Typically the data provided is
-a wrapper for the data of the solver itself, and the class info is a
-set of access functions that act on the data, with exactly the same interface
-as the original class. The messages of the zombified Element are left intact,
-with the possible exception of the 'process' message.
-
-To do zombification, the Element provides several handy functions:
-MsgId findCaller( fid ): Finds the first Msg that calls the specified fid.
-getInputMsgs( vector< MsgId >, Fid ): Finds all Msgs that call the fid.
-getOutputs< vector< Id >, const SrcFinfo* ): Finds all target Ids of the Src
-getInputs< vector< Id >, const DestFinfo* ): Finds all src Ids of the Dest
-zombieSwap( const Cinfo*, DataHandler* ): Replaces Cinfo and data on Element.
-
-The solver data class should provide utility functions for the Zombies to
-covert object Ids to lookup indices into the solver.
-
-
-Original Data is replaced completely with a solved version
-The Element uses a replacement Cinfo to handle this, so that the operation:
- OpFunc Element::getOpFunc( funcId ); // asks Cinfo for opFunc.
-is now redone. This handles all field access and async messages.
-< Need to work out what to do with sync messages >
-
-
-
-
-
-
-
-Slot::sendTo
- - Sets up a temporary buffer for the argument and target index.
- - only it doesn't use it. Could replace the target index stuff
- done below in Conn::tsend.
-Eref::tsend
- - Creates a Qinfo with the useSendTo flag
- - Element looks up a Conn based on ConnId.
-Conn::tsend
- - Looks for a Msg with a target Element matching the target Id.
- - Appends the target index after the arg in the buffer.
- - Updates the Qinfo to indicate the new size
-Msg::addToQ
- - the Qinfo gets the msgId of the target
-Element::addToQ
-Qinfo::addToQ called with the queue vector from the Element.
- - copies the Qinfo and then the arg into the queue.
-
-...................... There it sits till Element::clearQ
-
-Element::clearQ
- Marches through buffer
-Element::execFunc
- - Extracts Qinfo
- - Looks up func and Msg
- - If useSendTo:
- OpFunc::op Executes the function.
- - else:
- Msg::exec
- - Sorts out which target to use.
- Unnecessary as it is on it
- Opfunc::op: Executes the function.
-
-
-------------------------------------------------------------------------------
-Parallelism and grouping.
-After some analysis, it seems like many parallel simulations will have a
-lumpy connectivity. That is, there will be groups with high internal
-connectivity. Different groups and stray other elements have sparser
-connectivity. For example, a brain region (e.g., OB) will be highly connected
-internally, and much more loosely connected externally. So the OB would form
-one group, and perhaps the Piriform another group.
-
-Multithreading and MPI-based decomposition are very similar as one scales up:
-in both cases we need buffers for data transfer. Up to a point it makes sense
-to amalgamate all MPI based communication for each node even if it has many
-threads internally. This is the main asymmetry.
-
-------------------------------------------------------------------------------
-
-MULTITHREADING.
-Async:
-Setup:
-Nothing special
-Send:
-
-Each thread has a separate section of the Queue on each target Element. So
-there is never any need for individual mutexes.
-clearQ: Three possible levels of separation.
- - Separate at the level of Msgs for large Msgs handling lots of
- targets. Separate chunks of the targets could be assigned to
- different threads. Needs that no other threads are modifying target.
- - Separate at the level of Elements; so that each Element is on a
- different thread. Need to set up enough Elements to balance this
- properly. Can we set up multiple Elements on the same node with the
- same Id? This would work well for cases where there are huge numbers
- of Elements.
- - Separate at the level of solvers. Works where one big solver handles
- lots of Elements. This becomes very solver-specific, and we would
- have to define rules for how the solver is allowed to do this.
-Sync:
-No problems because the memory locations are distinct for all data transfer.
-
-Data transfer of 'group' queues, from perspective of each thread.
- - During process, put off-group stuff into off-group queues.
- - on-node other threads; and off-node data each have queues.
- - During process, put in-group data into own 'output' queue.
- - When Process is done, consolidate all in-group 'output' queues.
- - Send consolidated in-group queue to all nodes in group
- - off-group, on-node queues are handled by their owner threads.
- - Send off-group, off-node queues to target nodes.
- - Receive consolidated queues from on-group nodes.
- [further consolidate?]
- - Receive mythread input queue from off-group, on-node threads
- - Recieve anythread input queues from off-group off-node
- [Consolidate input queues ?]
- - Iterate through consolidated queue for in-group, on-node.
- - Iterate through consolidated queue for in-group, off-node.
- - Iterate through input queue for off-group, on-node
- - Iterate through input queue for off-group, off-node.
- - Each thread will have to pick subset of entries to handle.
-
-Data transfer of 'non-group' queues, from perspective of each thread:
- - During process, put off-group stuff into off-group queues.
- - on-node other threads; and off-node data each have queues.
- - During process, put own stuff into own input queue.
- - off-group, on-node queues are handled by their owner threads.
- - Send off-group, off-node queues to target nodes.
- - Receive mythread input queue from off-group, on-node threads
- - Recieve anythread input queues from off-group off-node
- [Consolidate input queues ?]
- - Iterate through input queue for off-group, on-node
- - Iterate through input queue for off-group, off-node.
- - Each thread will have to pick subset of entries to handle.
-
-.........................................................................
-Setting up multithread scheduling.
-For comparison, here is regular scheduling
-Shell::start:
- calls Clock::threadStartFunc( void* threadInfo ), no threads.
-Clock::threadStartFunc( void* threadInfo ) is the static thread function.
- calls Clock::Start in non-thread version, with args in threadInfo
-Clock::Start:
- If just one tickPtr: advance through the tickPtr for the entire time.
- If multiple tickPtrs (i.e., many dts):
- sort the tickPtrs
- loop while tickPtr[0].nextTime < endTime
- advance tickPtr0 till nextTime
- sort again
- update nextTime.
- *---*
-
-Multithread scheduling: Assume group-wise queue handling for now.
-Shell::start:
- Makes barrier. Spawns child threads, with threadStartFunc.
- Waits for them to join.
-Clock::threadStartFunc( void* threadInfo ) calls tStart in threaded version.
-Clock::tStart()
- if just one tickPtr, advance through it for the entire time.
- TickPtr::advance: loop while nextTime_ < endTime. In this loop,
- call all the Ticks (at different stages)
- Need to cleanly handle advancing of p->currTime and nextTime_,
- which are used by all threads. So this must be made thread-safe.
-
-
- Tick::advance():
- Qinfo::clearQ( threadId )
- Note that here there is a Q shared among
- all threads, and it is treated as readonly.
- Conn::process.
- Puts outgoing data into thread-local output Q.
- Condition: when all other threads are done, the
- Qs are either merged or put into a frame-buffer
- so that all threads can now handle entire
- set as readonly.
- Or, Barrier: Ensure all threads are done
- Thread 0: Merge Qs into a frame-buffer, set as readonly
- Barrier: Ensure thread0 is done before proceeding.
- Equivalently, the entry into the clearQ routine could
- be the synchronization point.
-
- If multiple tickPtrs:
-
-
-
-
- *---*
-
-Qinfo::readQ( threadId )
- Reads the data from threadId. It is entirely readonly, and is thread-
- safe. Different threads can use the same threadId.
-
-Qinfo::clearQ( threadId )
- Clears the data from threadId; that is, zeroes it out.
-
-The design sequence is that for
-
-------------------------------------------------------------------------------
-
-MPI:
-Async:
-Setup: need to figure out off-node targets. See below for send.
-
-Send:
-Msg has been preconfigured to add to the regular Q, the outgoing Q, or both.
-Shouldn't this be separate Msgs? But it is to the same Element, just to
-a different buffer on it.
-
-ClearQ:
-On-node stuff is as usual.
-Postmasters (or Elements themselves) clear out off-node Qs in a straightforward
-way, since everything is now serialized.
-Once these arrive on the target node, they simply get dumped into the incoming
-Q of the target Element.
-
-
-------------------------------------------------------------------------------
-
-Managing space, specially in chemical models.
-
-Conceptually, each Compartment is enclosed by one or more Geometry
-objects. There may or may not be an adjacent Compartment on the other
-side. The Compartment has a vector of Boundary objects, which are
-managed in a FieldElement.
-The geometry/adjacency relationships are defined by messages from the
-Boundary FieldElement.
-Compartments also have a 'size' and 'dimension'. I haven't yet worked
-out a general way to get this from an arbitrary set of Geometries
-around them, but in principle it can be obtained from this.
-Again, in principle, the size may change during a simulation.
-
diff --git a/moose-core/Docs/developer/Ksolve.txt b/moose-core/Docs/developer/Ksolve.txt
deleted file mode 100644
index 609752a09682a9a546ee9d259784e2704baf43bc..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/Ksolve.txt
+++ /dev/null
@@ -1,101 +0,0 @@
-API for Ksolve implementation
-
-Introduction.
-This part of the MOOSE documentation describes how fast linear algebra
-solutions of chemical reaction networks are carried out. The equations are
-a system of nonlinear ODEs defined as follows:
-
-dS/dt = N.v
-
-where S is the vector of molecule concentrations
-N is the stoichiometry matrix defining the reaction system, and v is the
-rate vector, that is, the vector of rates of each reaction in the system.
-The rows of N are molecules, and the columns are reactions.
-
-Numerics
-The actual calculations in the Ksolve are done using the GNU Scientific
-Library, GSL. The GSL offers a number of numerical methods, most of which
-are available to the Ksolver. The adaptive timestep Runge Kutta method rk5
-is usually a good choice.
-
-Other roles ofthe Ksolve system
-Other than the calculations, the key role played in the Ksolve is to interface
-between the Element and message-based model structure definition, and the
-contents of the various matrices and vectors that do the number crunching.
-This is in two phases:
-
-Setup: Here the ksolve system has to scan through the reaction system to build
-up the stoichiometry matrix and calculation rules for the rate vector.
-Runtime updates: Here the Ksolver has to respond to any requests from the
-MOOSE model structure for getting or setting values in the reaction sytem.
-
-In addition there are various elaborations for handling interfaces to other
-solvers and numerical engines, such as Smoldyn and the SigNeur system.
-
-
-=============================================================================
-
-System overview
-
-Classes:
-Stoich: Manages the data structures in the simulation. Specifically,
- molecule vector S
- initial conditions Sinit
- Reaction velocity vector v
- Stoichiometry matrix N
- Vector of rate terms rates
- Vector of function terms funcs
- Mapping from the Ids to S, rates, funcs objMap
-
- Also has key functions:
- Set up the model setPath()
- Update the reaction velocities updateV()
- Reinitializes conditions reinit()
- Note that process() is a dummy function.
-
-
-
-GslIntegrator: Numerical engine for Stoich, using the GSL.
- It has a few simulation control parameters
- method
- accuracy
- stepsize
- and it has a pointer to the stoich_ class.
- It also holds internal data structures for GSL.
-
- It does the actual calculations in the function:
- process
-
-
-KinSparseMatrix: Efficiently holds the stoichiometry matrix.
- Derived from SparseMatrix< int >
- Provides efficient compute operations for getting dS/dt from the
- molecule vector and the reaction velocity vector.
- It has some hooks for doing Gillespie type calculations too.
-
-RateTerm: Base class for a large number of derived classes which compute
- derivatives for various kinds of reactions, like enzymatic,
- reversible, and so on. Looks up molecule amounts by their indices in
- the Stoich::S vector.
-
-FuncTerm: Base class for assorted derived classes which compute
- functions based on molecule arguments looked up by their indices.
-
-
-Zombie classes:
- These are all derived from the Stoich, and have no C++ fields of their
- own. Instead they have the MOOSE fields of the class that they
- are taking over.
-
- At setup, the 'zombify' function takes all the relevant parameters
- from the original object, puts them into the Stoich, and replaces
- the 'data' part of the original object with the Zombie version.
- Thus all the original messages and Ids are unchanged.
-
- There is an 'unzombify' function which supposedly does the reverse,
- but it hasn't been rigorously tested.
-
- In operation, all fields and functions of the zombified class are
- handled by accessing the corresponding Stoich fields.
-
-=============================================================================
diff --git a/moose-core/Docs/developer/MessageObjectLookup.txt b/moose-core/Docs/developer/MessageObjectLookup.txt
deleted file mode 100644
index 8cdde37ae8c890b647a1e6ae4484df9639fbfc36..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/MessageObjectLookup.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-How to go from Msg to corresponding Element and object, and back.
-
-The system sets up a set of Manager Elements, one for each Msg subclass
-(Single, OneToAll, Sparse, and so on).
-These Manager Elements are OneDimGlobals, that is, an array.
-The Manager base data class is just a MsgId (with some added functions).
-
-So every time a message is created, it figures out which Manager it belongs to,
-and pushes back its MsgId onto the array. The Msg constructor calls
-MsgManager::addmsg( MsgId mid, Id managerId ).
-
-
-There is a static vector of unsigned ints, Msg::lookUpDataId_, indexed by
-msgid, to look up the dataIds for each msg. So:
-Msg to DataId: Msg::lookUpDataId_[msg->msgid]
-
-object to msg: Msg::safeGetMsg( getMid() );
-where the getMid function just returns the mid_ value of the MsgManager.
-
-In use, the derived MsgManager, such as SparseMsgWrapper, typecasts the Msg to
-the appropriate type and does stuff with it.
-
-
diff --git a/moose-core/Docs/developer/PortingOldMooseObjects.txt b/moose-core/Docs/developer/PortingOldMooseObjects.txt
deleted file mode 100644
index abbc552daa4444808df58ed2600bd1e77f2e11ef..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/PortingOldMooseObjects.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-1. In the initCinfo function, at the end where the static Cinfo is created,
-we need to make the Dinfo allocation a static one.
-
-1a. above the static Cinfo function, add a line
- static Dinfo< T > dinfo;
-1b. Replace the line
- new Dinfo< T >()
- with
- &dinfo
-
-2. Eliminate all instances of Qinfo. Some functions may pass it in as an
-argument, just eliminate the argument.
-
-3. In 'send' calls, eliminate the threadInfo argument.
-
-4. Check that you are consistent with the naming scheme for all SrcFinfos:
- they must have a suffix 'Out'.
-
-5. Use Element-level operations with care. Many commands
-are strictly per-node, and will do odd things if invoked in parallel.
-id(), getName(), numData(), getNode(), hasFields(), isGlobal() and
-getNumOnNode() are safe on any node. But don't try to do any data access
-operations. Use SetGet calls for data access.
-
-6. In the unlikely event that you are dealing with Zombies, the Zombie
-handling has changed. Now the ZombieSwap function just takes the new
-Cinfo and does three things:
- - allocates new data with this new Cinfo, using the same size.
- - deletes the old data
- - Replaces the Cinfo.
-This means that if you want to transfer any values over from the old to the
-new class, you need to extract the values first, zombify, and then put them
-into the new class.
-
-7. In the even less likely event that you are dealing with DataHandlers,
- talk to Upi. The DataHandlers have been eliminated.
diff --git a/moose-core/Docs/developer/PythonRecommendations.org b/moose-core/Docs/developer/PythonRecommendations.org
deleted file mode 100644
index 370451e7aafeb42fe718ef87b4085ef36d58fa4b..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/PythonRecommendations.org
+++ /dev/null
@@ -1,135 +0,0 @@
-#+TITLE: Recommended coding practices for Python scripting
-Python is a very flexible scripting language with very few rules
-imposed by the language designers. Thus you are free to shoot yourself
-in the foot any way you like and nobody is going to stop you. A
-popular slogan summarizing the Python philosophy is "We are all
-consenting adults here".
-
-But not everybody who writes code is an "adult" in the programming
-sense. And even seasoned programmers have a tendency to get entangled
-by their own "smart" code to render them immobile
-(programmatically). Time and again we need to be reminded of the
-basics.
-
-There are some pretty common ideas that keep coming up in various
-mailing list discussions and here is a collection of aphorisms, tips,
-tricks and links to such things.
-
-* KISS: Keep it short and simple
-** Logical program units should fit in one screen
- That is not a hard limit, but if your function definition is too
- long then you may want to rethink it. A function should do one well
- defined task. Check your function to see if you have put in
- multiple disparate tasks inside one function.
-
- See
- [[http://stackoverflow.com/questions/475675/when-is-a-function-too-long]]
-
-** More than five logical units at any level is too much
- Remember that code has to be read and understood by average human
- beings. And five to seven is the number of items most people can
- easily keep in mind. So it is a good idea to compose things with
- those many elements. Think of data flow diagrams.
-
-** "If you need more than 3 levels of indentation, you're screwed anyway, and should fix your program."
- That was Linus Torvalds in 1995. While it sounds a bit drastic,
- loops nested more than three levels need serious
- consideration. Most likely you can find a better way to write that
- code if you think hard enough.
-
-** "Everyone knows that debugging is twice as hard as writing a program in the first place. So if you're as clever as you can be when you write it, how will you ever debug it?"
- - Brian Kernighan.
-
- What you thought was a clever trick is likely to cause a lot of
- pain in future. If it is too clever, two weeks down the line you
- will most probably have no clue how it works. Forget about other
- people reading your code being able to understand your code. If you
- think the trick is really necessary, document it!
-
-** Write idiomatic code
- Like natural (human) languages programming languages also gather
- standard idioms. Some ways of programming turn out to be so useful
- that everybody starts using them. You will be more productive in a
- new programming language (and more readable to your fellow
- programmers) if you master these idioms. A nice collection of such
- idioms for Python is available here:
- [[http://python.net/~goodger/projects/pycon/2007/idiomatic/handout.html]]
-
-* Document
-** "You know you're brilliant, but maybe you'd like to understand what you did 2 weeks from now."
- - Linus Torvalds.
-
- While most software companies reuire their programmers to document
- their work, many beginning hackers and academic programmers think
- "I know what I am doing! I know this code inside out, there is no
- need for documentation." As Linus correctly pointed out, you, two
- weeks from writing a piece of code, are a different person from the
- one who wrote it. And if your code was too clever, most likely you
- will not be understand it later (here comes the quote by Brian
- Kernighan). So better document your code for your own good.
-
-* Think
-** Before you write anything, think!
- It is often better to make rough outlines using pen and paper
- before you start typing your code. Just like writing an essay or a
- novel, programs need a coherent flow of thought, and an outline
- helps with that.
-
-** "The most effective debugging tool is still careful thought, coupled with judiciously placed print statements."
- Brian Kernighan wrote that in 1979 and it still applies no matter
- how proficient you are with gdb or some other debugger. Jumping
- into a debugger without re-reading your code is a sure sign that
- you are not using your brain properly. A debugger can help you
- narrow down the code you need to investigate, but usually a second
- reading of your code (better after a break) is the most efficient
- and educational way to find and fix a bug.
-
-* Fast Python: Some points regarding performance for more advanced users (but good to practice these from the beginning)!
-** These points are quoted from a post by Guido van Rossum on Google+ on 11 Sep 2012
- - Avoid overengineering datastructures. Tuples are better than
- objects (try namedtuple too though). Prefer simple fields over
- getter/setter functions.
-
- - Built-in datatypes are your friends. Use more numbers, strings,
- tuples, lists, sets, dicts. Also check out the collections
- library, esp. deque.
-
- - Be suspicious of function/method calls; creating a stack frame is
- expensive.
-
- - Don't write Java (or C++, or Javascript, ...) in Python.
-
- - Are you sure it's too slow? Profile before optimizing!
-
- - The universal speed-up is rewriting small bits of code in C. Do
- this only when all else fails.
-
- - I'm -0 on using generator[ expression]s unless you know you have
- huge lists of values to iterate over. The concrete list
- [comprehension] is usually faster than the genexpr until memory
- allocation becomes critical.
-
-** Michael Foord added the following points to the same post by Guido
- Understand the performance characteristics of basic operations on
- the builtin types. For example
-
- - Checking for membership in a list is O(N) but for a set or
- dictionary it is O(1).
-
- - Adding lists and tuples creates new objects.
-
- - Inserting to the left of a list is O(N) whilst append is O(1)
- (use a deque instead). And so on.
-
-** Richard Merren added to the same post by Guido
- - Use dicts to store and retrieve information--they are very fast.
-
- - Break your task up to simple and testable/verifiable functions so
- that you make less errors on each part.
-
- - Don't be afraid to give variables and functions long and
- descriptive names so you can reread your code and figure out what
- it does.
-
- - Do things the way they make sense to you and don't worry about
- optimizing your code until you find out which part is slow.
diff --git a/moose-core/Docs/developer/ReduceOperations b/moose-core/Docs/developer/ReduceOperations
deleted file mode 100644
index d1206523f18627a6ddc6a32000e5c4cb45a1cd2c..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/ReduceOperations
+++ /dev/null
@@ -1,154 +0,0 @@
-Overview
-Reduce operations are those that scan through many objects, condensing some
-attribute into a reduced form. For example, we might use a reduce operation to
-compute statistics on Vm across neurons in a population in a model
-spread across multiple nodes. Another common use is to keep track of the
-max field dimension in a variable size field such as the number of synapses on
-a channel or an IntFire neuron.
-
-
-There are two modes of operation:
-1. through a regular Reduce Msg, originating from a ReduceFinfo on a regular
-object, and terminating on any 'get' DestFinfo. ReduceFinfos are derived from
-SrcFinfos. They are templated on the type of the 'get' function, and on
-the type of the reduce class (for example, a triad of mean, variance and count).
-The ReduceFinfo constructor takes as an argument a 'digest' function. The
-job of the digest function is to take an argument of the reduce class
-(which has the contents of the entire reduction operation),
-and do something with it (such as saving values into the originating object).
-
-2. Through Shell::doSyncDataHandler. This takes the synced Elm and its
-FieldElement as Ids, and a string for the field to be reduced, assumed an
-unsigned int. It creates a temporary ReduceMsg from the Shell to the Elm with
-the field to be reduced. Here the digest function just takes the returned
-ReduceMax< uint > and puts the max value in Shell::maxIndex. It then posts
-the ack. The calling Shell::doSyncDataHandler waits for the ack, and when it
-comes, it calls a 'set' function to put the returned value into the
-FieldDataHandler::fieldDimension_.
-
-At some point I may want to embed the doSyncDataHandler into any of the
-'set' functions that invalidate fieldDimension. Problem is race conditions,
-where a set function would call the doSync stuff which internally has its
-own call to Ack-protected functions, like 'set'. Must fix.
-
-
-
-The setup of the Reduce functionality is like this:
-
-- Create and define the ReduceFinfo.
- ReduceFinfo< T, F, R >( const string& name, const string& doc,
- void ( T::*digestFunc )( const Eref& er, const R* arg )
- Here T is the type of the object that is the src of the ReduceMsg,
- F is the type of the returned reduded field
- R is the Reduce class.
-
-- Create and define the ReduceClass. This does two things:
- - Hold the data being reduced
- - Provide three functions, for primaryReduce, secondaryReduce, and
- tertiraryReduce. We'll come to these in a little while.
-
--
--
-
-
-When executing reduce operations from the Shell::doSyncDataHandler, this
- is what happens:
-- Shell::doSyncDataHander does some checking, then
- requestSync.send launches the request, and waits for ack
- - Shell::handleSync handles the request on each node
- - Creates a temporary ReduceMsg from Shell to target elm
- - The ReduceMsg includes a pointer to a const ReduceFinfoBase*
- which provides two functions:
- - makeReduce, which makes the ReduceBase object
- - digestReduce, which refers to the digestFunc of
- the calling object.
- - Sends a call with a zero arg on this Msg.
- - Msg is handled by ReduceMsg::exec.
- - This extracts the fid, which points to a getOpFunc.
- - It creates the derived ReduceBase object.
- - It adds the ReduceBase object into the ReduceQ
- - indexed by thread# so no data overwrites.
- - It scans through all targets on current thread and uses the
- derived virtual function for ReduceBase::primaryReduce
- on each.
- Overall, for each thread, the 'get' values get reduced and stored
- into the ReduceBase derived class in the queue. There is such an
- object for each thread.
-
- - Nasty scheduling ensues for clearing the ReduceQ.
- - in Barrier 3, we call Clock::checkProcState
- - this calls Qinfo::clearReduceQ
- - This marches through each thread on each reduceQ entry
- - Uses the ReduceBase entry from the zeroth thread
- as a handle.
- - Calls ReduceBase::secondaryReduce on each entry for
- each thread.
- - This is done in an ugly way using
- findMatchingReduceEntry, could be cleaned up.
- - Calls ReduceBase::reduceNodes
- - If MPI is running this does an instantaneous
- MPI_Allgather with the contents of the
- ReduceBase data.
- - Does ReduceBase::tertiaryReduce on the received data
-/// New version
- - calls Element::setFieldDimension directly using ptr.
-/// End of new stuff
- - returns isDataHere.
-
-
- - If reduceNodes returns true, calls ReduceBase::assignResult
- - This calls the digestReduce function, which is
- Shell::digestReduceMax
-
-////////////////////////////////////////////////////////////////////////
-// Old version
- - Shell::digestReduceMax assigns maxIndex_ and sends ack
- - ack allows doSyncDataHandler to proceed
- - calls Field::set on all tgts to set "fieldDimension" to maxIndex_.
-////////////////////////////////////////////////////////////////////////
- - Should really do a direct ptr assignment, within the
- assignResult function: Assume here that we want the assignment
- to be reflected on all nodes.
-
-The current code is grotty on several fronts:
- - The findMatchingReduceEntry stuff could be fixed using a more
- sensible indexing.
- - Should use direct ptr assignment for fieldDimension within
- assignResult.
- - I probably don't need to pass in both the FieldElement and its parent.
-
-When executing reduce operations from messages, this is what happens:
-- ReduceFinfo.send launches the request. No args.
- - The ReduceMsg::exec function (which is called per thread):
- - This extracts the fid, which points to a getOpFunc.
- - It creates the derived ReduceBase object.
- - It adds the ReduceBase object into the ReduceQ
- - indexed by thread# so no data overwrites.
- - It scans through all targets on current thread and uses the
- derived virtual function for ReduceBase::primaryReduce
- on each.
- - Now we go again to the scheduling system to clear ReduceQ.
- - in Barrier 3, we call Clock::checkProcState
- - this calls Qinfo::clearReduceQ
- - This marches through each thread on each reduceQ entry
- - Uses the ReduceBase entry from the zeroth thread
- as a handle.
- - Calls ReduceBase::secondaryReduce on each entry for
- each thread.
- - This is done in an ugly way using
- findMatchingReduceEntry, could be cleaned up.
- - Calls ReduceBase::reduceNodes
- - If MPI is running this does an instantaneous
- MPI_Allgather with the contents of the
- ReduceBase data.
- - Does ReduceBase::tertiaryReduce on the received data
- - returns isDataHere.
-
- - If reduceNodes returns true, calls ReduceBase::assignResult
- on the originating Element.
- - This calls the digestReduce function, which is
- what was given to the ReduceFinfo when it was created.
- - This does whatever field assignments are needed,
- internally to the originating element which asked for
- the field values.
- Note no acks. It happens in Barrier 3 is all.
diff --git a/moose-core/Docs/developer/Scheduling.txt b/moose-core/Docs/developer/Scheduling.txt
deleted file mode 100644
index 9c8b02a2854f7211dfe15b0bf96e6049e5787a53..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/Scheduling.txt
+++ /dev/null
@@ -1,145 +0,0 @@
-This section describes the MOOSE multithreaded scheduling and how it
-interfaces with the parser, the Shell, and with MPI calls to other nodes.
-
-The code for this is mostly in shell/ProcessLoop.cpp.
-
-
-Overview:
-MOOSE sets off a number of threads on each node. If the machine has C cores,
-then C threads are used for computing, 1 thread is used for managing MPI
-data transfer, and 1 thread is used on node 0 only for interfacing between
-the Shell and the Parser. The number of compute threads C can be overridden on
-the command line, but defaults to the number of hardware cores.
-
-All threads go through process loops. As long as MOOSE is running, the system
-keeps the threads going through process loops, and keeps them in sync through
-three barriers per cycle around the loop.
-
-Barriers are checkpoints where the system guarantees that each
-thread will wait till all threads have arrived. MOOSE barriers differ from
-regular Pthreads barriers in that there is a special, single-thread function
-executed within each barrier. You can think of the net effect of a bundle of
-wires which have tight ties (barriers) at three points. Between the ties
-the wires hang loose and do their own calculations, but everything is brought
-into sync at the ties.
-
-When MOOSE is idling, all these threads continue but the Process call does
-not get sent to compute objects.
-
-When MOOSE is running a calculation, then the Process call does get issued.
-
-
-Details:
-
-As long as MOOSE is running, and whether or not it is doing a simulation,
-the following process loop operates:
-
-
-Stage Thread# Description
-Phase 1 0:C-1 Carry out Process calculations on all simulated objects
- C Do nothing.
- C+1 On node 0 only: Lock mutex for input from parser.
-
-Barrier1 Single Clear StructuralQ. This accumulates operations
- which alter the structure of the simulation, and thus
- must be done single-threaded.
- Swap inQ and outQ.
- At the end of this barrier, all Process calculations
- are all done and have sent their messages. Structural
- operations have been done. The
- message queues have been swapped so that data is
- ready to be read and acted upon.
-
-Phase 2 0:C-1 Clocks juggle the Ticks (on thread 0 only).
- Deliver and execute local node messages.
- Go into a loop to handle off-node messages.
- C Go into a loop to broadcast/receive all off-node msgs,
- one node at a time.
- This has to be done with a predetermined data block
- size, which is judged as a bit over the median data
- size. On the occasions where the data to come is bigger
- than this block, there is an immediate resend initiated
- that transfers the bigger block.
- At present we don't have dynamic resizing of the
- median block size, but it should not be hard to set up.
- C+1 On node 0 only: Do nothing.
-
-Barrier 2 Single Swap mpiInQ and mpiRecvQ. This barrier is encountered
- in the same loop as Phase 2, once for each node.
- At the end of each round through this barrier, all
- off-node messages on the indexed node have been sent,
- received, and acted upon.
-
-Phase 3 0:C-1 Complete execution for last node.
- C Do nothing
- C+1 Unlock the mutex for input from parser
-
-Barrier 3 Single Clear reduce operations, that is, operations where each
- thread and each node collates information and reduces it
- to a single quantity to go to either the master node
- or to all nodes.
- Change Clock state, between run, reinit, stop etc.
- At the end of this barrier, all messages from all
- nodes have been handled. The Clock knows what to
- do for the next cycle. Typicaly it goes back to Phase 1.
-
-Messaging, scheduling, and threads:
-Broadly, at any instant during the Phases, there are two available Queues:
-the inQ and the outQ.
-InQ: The inQ is a single, readonly, collated queue which
-is updated during Barrier 1. inQ has all the data from all the threads, and
-all the compute threads read it. It also contains all the data that needs to
-go off-node.
-outQ: The outQ is subdivided into one writable queue per thread, so there is
-no chance of overwriting data. Starting from Phase 2, the outQ accumulates
-messaging entries. This can be from messages sent in response to other
-messages in Phase 2, or more commonly from messages sent during the Process
-operation in Phase 1. Finally, in Barrier1 at swapQ, all the content from
-all the outQs is stitched together to make up the inQ, and all the subQs from
-the outQ are cleared.
-
-This same theme is repeated between nodes. The mpiInQ is the collated Q that
-has arrived from the sending node, and its contents are identical to the inQ
-of the sending node. The mpiRecvQ is a buffer sitting waiting for the next
-cycle of data to come from the next node.
-
-
-Clocks and scheduling.
-
-The Clock class coordinates the operation of a vector of Ticks. There
-is a single Clock object ( ClockId = 1 ) in the simulation.
-The Tick objects are present in an array on the Clock. Each Tick has a
-timestep (dt), and connects to a target Elements through messages.
-Unlike regular messages, which send their requests through the Queueing system,
-the Tick directly traverses through all messages, and calls the
-'process' function on the target Elements. This hands it down to the
-DataHandler, which iterates through all the target objects within the Element,
-and calls the specified Process function. Any function having the
-appropriate arguments could be called here. This is how different phases of
-Process, as well as Reinit, are called through the same mechanism.
-
-
-In Phase 1:
-The Clock and its child Ticks are called in parallel by all the threads. The
-thread decomposition is done by the DataHandler.
-
-In Phase 2:
-On thread 0 only, the Clock handles advancing of timesteps on Phase 2.
- After each Tick is called, it advances its current Time by dt.
- The sequencing for advancing Tick timings is done by the Clock, by
- brute force sorting of the Ticks after every pass through the Process
- loop.
- Ticks are sorted first by dt, and if that is the same, by their
- own index. So if Tick 2 and 3 have the same dt, Tick 2 will always
- be called first.
-
-In Barrier 3:
-The Clock executes Clock::checkProcState, which among other things decides
-whether to keep doing what it was (typically running Process or idling).
-Calls to alter ProcState are called only during phase 2, typically resulting
-from the Shell sending messages to the clock to do things.
-
-Reinit goes through almost identical phases and operations as the steps
- for advancing the simulation. The main difference is that the
- function called on the target objects at Reinit, is of course, reinit.
-
diff --git a/moose-core/Docs/developer/doxygen-API.cpp b/moose-core/Docs/developer/doxygen-API.cpp
deleted file mode 100644
index 6511ba0741baa04dbda7dca2e3acf068502cb654..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/doxygen-API.cpp
+++ /dev/null
@@ -1,408 +0,0 @@
-/**
-\page AppProgInterface Applications Programming Interface, API. Async13 branch.
-
-\section DataStructs Key Data structures
-\subsection DataStructOverview Overview
-MOOSE represents all simulation concepts through objects. The API specifies
-how to manipulate these objects. Specifically, it deals with their
-creation, destruction, field access, computation, and exchange of data
-through messages.
-
-Objects in MOOSE are always wrapped in the Element container class.
-Each Element holds an array of Objects, sized from zero to a very large
-number limited only by machine memory.
-
-The functions and fields of each class in MOOSE are defined in Finfos:
-Field Info classes. These are visible to users as fields.
-
-Data communication between Elements (that is, their constitutent Objects)
-is managed by the Msg class: messages.
-
-These three concepts: Elements, Finfos, and Msgs - are manipulated by
-the API.
-
-\subsection DataStructElementAccess Id: Handles for Elements
-
-Each Element is uniquely identified by an \b Id. Ids are consistent
-across all nodes and threads of a multiprocessor simulation. Ids are
-basically indices to a master array of all Elements. Ids are used by
-the Python system too.
-
-\subsection DataStructElementClasses Element classes: Handling Objects within elements.
-The \b Element is a virtual base class that manages objects.
-It deals with creation, resizing, lookup and
-destruction of the data. It handles load balancing. It manages fields.
-It manages messages.
-
-\subsection DataStructObjectClasses Object classes: Computational and data entities in MOOSE.
-\b Objects in MOOSE do the actual work of computation and data structures. They
-are insulated from the housekeeping jobs of creation, interfacing to scripts
-and to messaging. To do this they present a very stereotyped interface to
-the MOOSE Element wrapper. The following are the essential components of this
-interface. These are discussed in more detail in the document
-"Building New MOOSE Classes."
-\subsubsection ObjectsInMooseConstructor Object Constructors
-All MOOSE classes need a constructor \b Object() that correctly initializes
-all fields. This constructor does not take any arguments. It can be omitted
-only if the default C++ constructor will guarantee initialization.
-\subsubsection ObjectsInMooseAssignment Object assignment operator
-MOOSE needs to know how to copy objects. By default it does a bit-copy.
-If this is not what you need, then you must explicitly specify an assignment
-operator. For example, if you set up pointers and do not want your objects
-to share the data in the pointers, you will want to specify an assignment
-operator to rebuild the contents of the pointers.
-\subsubsection ObjectsInMooseFinfo Object fields.
-MOOSE needs to know what fields an object has. Fields can be of three main
-kinds: value fields, message source fields, and message destination
-(aka function) fields. All these fields are managed by \b Finfo objects
-(Field infos), which are in turn organized by the Cinfo (Class Info) objects
-as described below. In a nutshell, all fields are associated with a name,
-access functions, and some documentation by creating Finfos for them, and
-all the Finfos are stored in the Cinfo.
-\subsubsection ObjectsInMooseCinfo Object class information.
-Every MOOSE class is managed by a \b Cinfo (Class Info) object. This is defined
-in a static initializer function in every class. The Cinfo stores
-the class name and documentation, how to look up fields, how to
-handle data, and so on.
-\subsubsection ObjectsInMooseMsgs Object message sending.
-Any MOOSE object can call any function in any other object. This is managed
-by the message source fields: \b SrcFinfos. SrcFinfos defined as above all
-present a \b send() function, which traverses all targets of the message and
-calls the target function with the specified arguments. SrcFinfos are typed, so
-precisely the correct number and type of arguments are always sent. Messages
-can go across nodes, the user does not need to do anything special to
-arrange this.
-
-\subsection DataStructObjectAccess ObjId: Identifiers for Objects within elements.
-
-The \b ObjId specifies a specific object within the Element. All Elements
-manage a linear array of identical objects, which can have any number of
-entries greater than zero, up to the limits of memory. The ObjId::dataIndex
-field is the index into this array.
-In addition, the ObjId has a field ObjId::fieldIndex that comes into use in a
-subset of objects. This is used when each object has to manage arrays of
-fields, which are made visible as FieldElements. For example, one could have
-an array of receptor channels, each of which manages an array of synapses.
-Thus to fully specify a synapse, one uses both the ObjId::dataIndex to
-specify the parent receptor, and the ObjId::fieldIndex to specify the synapse
-on that receptor.
-
-\subsection DataStructObjId ObjId: Fully specified handle for objects.
-
-The ObjId is a composite of Id and DataId. It uniquely specifies any
-entity in the simulation. It is consistent across nodes.
-In general, one would use the ObjId for most Object manipulation,
-field access, and messaging API calls.
-The ObjId can be initialized using a string path of an object.
-The string path of an object can be looked up from its ObjId.
-
-\subsection DataStructTrees Element hierarchies and path specifiers.
-Elements are organized into a tree hierarchy, much like a Unix file
-system. This is similar to the organization in GENESIS. Since every
-Element has a name, it is possible to traverse the hierarchy by specifying
-a path. For example, you might access a specific dendrite on cell 72 as
-follows:
-
-\verbatim
-/network/cell[72]/dendrite[50]
-\endverbatim
-
-Note that this path specifier maps onto a single ObjId.
-Every object can be indexed, and if no index is given then it assumed
-that it refers to index zero. For example, the above path is identical
-to:
-
-\verbatim
-/network[0]/cell[72]/dendrite[50]
-\endverbatim
-
-Path specifiers can be arbitrarily nested. Additionally, one can have
-single dimensional arrays at any level of nesting. Here is an example
-path with nested arrays:
-
-\verbatim
-/network/layerIV/cell[23]/dendrite[50]/synchan/synapse[1234]
-\endverbatim
-
-\subsection ObjIdAndPaths ObjIds, paths, and dimensions.
-Objects sit on the Elements, which follow a tree hierarchy. There are
-two ways to find an object.
-First, the ObjId completely identifies an object no matter where it is in
-the object tree.
-Second, one can traverse the Element tree using indices to identify
-specific Objects. This too uniquely identifies each Object.
-Every ObjId has a 'parent' ObjId, the exception being the root ObjId
-which is its own parent.
-Any ObjId can have its own 'child' objects in the tree.
-The tree cannot loop back onto itself.
-Objects are always stored as linear arrays.
-
-\verbatim
-/foo[0]/bar
-\endverbatim
-is a different object from
-\verbatim
-/foo[1]/bar
-\endverbatim
-
-Some useful API calls for dealing with the path:
-
-ObjId::ObjId( const string& path ): Creates the ObjId pointing to an
- already created object on the specified path.
-
-string ObjId::path(): Returns the path string for the specified ObjId.
-
-\verbatim
-ObjId f2( "/f1[2]/f2" );
-assert( f2.path() == "/f1[2]/f2[0]" );
-\endverbatim
-
-There is a special meaning for the path for synapses. Recall that the
-ObjId for synapses (which are FieldElements of SynChans) has two
-indices, the DataIndex and the FieldIndex. The DataIndex of the
-synapse is identical to that of its parent SynChan.
-This is illustrated as follows:
-
-\verbatim
-ObjId synchan( "/cell/synchan[20] );
-assert( synchan.dataIndex == 20 );
-
-ObjId synapse( "/cell/synchan[20]/synapse[5]" );
-assert( synapse.dataIndex == 20 );
-assert( synapse.fieldIndex == 5 );
-\endverbatim
-
-\subsection Wildcard_paths Wildcard paths
-Some commands take a \e wildcard path. This compactly specifies a large
-number of ObjIds. Some example wildcards are
-
-\verbatim
-/network/## // All possible children of network, followed recursively
-/network/# // All children of network, only one level.
-/network/ce# // All children of network whose name starts with 'ce'
-/network/cell/dendrite[] // All dendrites, regardless of index
-/network/##[ISA=CaConc] // All descendants of network of class CaConc
-/soma,/axon // The elements soma and axon
-\endverbatim
-
-
-\section FieldAccess Setting and Getting Field values.
-\subsection FieldAccessOverview Overview
-There is a family of classes for setting and getting Field values.
-These are the
-\li SetGet< A1, A2... >::set( ObjId id, const string& name, arg1, arg2... )
-and
-\li SetGet< A >::get( ObjId id, const string& name )
-functions. Here A1, A2 are the templated classes of function arguments.
-A is the return class from the \e get call.
-
-Since Fields are synonymous with functions of MOOSE objects,
-the \e set family of commands is also used for calling object functions.
-Note that the \e set functions do not have a return value.
-
-The reason there has to be a family of classes is that all functions in
-MOOSE are strongly typed. Thus there are SetGet classes for up to six
-arguments.
-
-
-\subsection FieldAccessExamples Examples of field access.
-1. If you want to call a function foo( int A, double B ) on
-ObjId oid, you would do:
-
-\verbatim
- SetGet2< int, double >::set( oid, "foo", A, B );
-\endverbatim
-
-2. To call a function bar( int A, double B, string C ) on oid:
-\verbatim
- SetGet3< int, double, string >::set( oid, "bar", A, B, C );
-\endverbatim
-
-3. To assign a field value "short abc" on object oid:
-\verbatim
- Field< short >::set( oid, "abc", 123 );
-\endverbatim
-
-4. To get a field value "double pqr" on object oid:
-\verbatim
- double x = Field< short >::get( oid, "pqr" );
-\endverbatim
-
-5. To assign the double 'xcoord' field on all the objects on
-element Id id, which has an array of the objects:
-\verbatim
- vector< double > newXcoord;
- // Fill up the vector here.
- Field< double >::setVec( id, "xcoord", newXcoord );
-\endverbatim
- Note that the dimensions of newXcoord should match those of
- the target element.
-
- You can also use a similar call if it is just a function on id:
-\verbatim
- SetGet1< double >::setVec( id, "xcoord_func", newXcoord );
-\endverbatim
-
-6. To extract the double vector 'ycoord' field from all the objects on id:
-\verbatim
- vector< double > oldYcoord; // Do not need to allocate.
- Field< double >::getVec( id, "ycoord", oldYcoord );
-\endverbatim
-
-7. To set/get LookupFields, that is fields which have an index to lookup:
-\verbatim
- double x = LookupField< unsigned int, double >::get( objId, field, index );
- LookupField< unsigned int, double >::set( objId, field, index, value );
-\endverbatim
-
-\section APIcalls API system calls
-\subsection FieldAccessOverview Overview
-There is a special set of calls on the Shell object, which function as the
-main MOOSE programmatic API. These calls are all prefixed with 'do'. Here is
-the list of functions:
-
-\li Id doCreate( string type, Id parent, string name, vector< unsigned int > dimensions );
-\li bool doDelete( Id id )
-\li MsgId doAddMsg( const string& msgType, ObjId src, const string& srcField, ObjId dest, const string& destField);
-\li void doQuit();
-\li void doStart( double runtime );
-\li void doReinit();
-\li void doStop();
-\li void doMove( Id orig, Id newParent );
-\li Id doCopyId orig, Id newParent, string newName, unsigned int n, bool copyExtMsgs);
-\li Id doFind( const string& path ) const
-\li void doSetClock( unsigned int tickNum, double dt )
-\li void doUseClock( string path, string field, unsigned int tick );
-\li Id doLoadModel( const string& fname, const string& modelpath );
-
-
-
-\section ClockScheduling Clocks, Ticks, and Scheduling
-\subsection ClockOverview Overview
-Most of the computation in MOOSE occurs in a special function called
-\e process,
-which is implemented in all object classes that advance their internal
-state over time. The role of Clocks and Ticks is to set up the sequence of
-calling \e process for different objects, which may have different intervals
-for updating their internal state. The design of scheduling in moose is
-similar to GENESIS.
-
-As a simple example, suppose we had six objects, which had to advance their
-internal state with the following intervals:
-\li \b A: 5
-\li \b B: 2
-\li \b C: 2
-\li \b D: 1
-\li \b E: 3
-\li \b F: 5
-
-Suppose we had to run this for 10 seconds. The desired order of updates
-would be:
-
-\verbatim
-Time Objects called
-1 D
-2 D,B,C
-3 D,E
-4 D,B,C
-5 D,A,F
-6 D,B,C,E
-7 D
-8 D,B,C
-9 D,E
-10 D,B,C,A,F
-\endverbatim
-
-\subsection ClockReinit Reinit: Reinitializing state variables.
-In addition to advancing the simulation, the Clocks and Ticks play a closely
-related role in setting initial conditions. It is required that every object
-that has a \e process call, must have a matching \e reinit function. When the
-command \e doReinit is given from the shell, the simulation is reinitialized
-to its boundary conditions. To do so, the \e reinit function is called in the
-same sequence that the \process would have been called at time 0 (zero).
-For the example above, this sequence would be:\n
-D,B,C,E,A,F
-
-In other words, the ordering is first by dt for the object, and second by
-the sequence of the object in the list.
-
-During reinit, the object is expected to restore all state variables to their
-boundary condition. Objects typically also send out messages during reinit
-to specify this boundary condition value to dependent objects. For example,
-a compartment would be expected to send its initial \e Vm value out to a
-graph object to indicate its starting value.
-
-\subsection ClockSetup Setting up scheduling
-The API for setting up scheduling is as follows:\n
-1. Create the objects to be scheduled.\n
-2. Create Clock Ticks for each time interval using
-
-\verbatim
- doSetClock( TickNumber, dt ).
-\endverbatim
-
-In many cases it is necessary to have a precise sequence of events
-ocurring at the same time interval. In this case, set up two or more
-Clock Ticks with the same dt but successive TickNumbers. They will
-execute in the same order as their TickNumber. \n
-Note that TickNumbers are unique. If you reuse a TickNumber, all that
-will happen is that its previous value of dt will be overridden.
-
-Note also that dt can be any positive decimal number, and does not
-have to be a multiple of any other dt.
-
-3. Connect up the scheduled objects to their clock ticks:
-
-\verbatim
- doUseClock( path, function, TickNumber )
-\endverbatim
-
-Here the \e path is a wildcard path that can specify any numer of objects.\n
-The \e function is the name of the \e process message that is to be used. This
-is provided because some objects may have multiple \e process messages.
-The \e TickNumber identifies which tick to use.
-
-Note that as soon as the \e doUseClock function is issued, both the
-\e process and \e reinit functions are managed by the scheduler as discussed
-above.
-
-\subsection ClockSchedExample Example of scheduling.
-As an example, here we set up the scheduling for the same
-set of objects A to F we have discussed above.\n
-First we set up the clocks:
-
-\verbatim
- doSetClock( 0, 1 );
- doSetClock( 1, 2 );
- doSetClock( 2, 3 );
- doSetClock( 3, 5 );
-\endverbatim
-
-Now we connect up the relevant objects to them.
-
-\verbatim
- doUseClock( "D", "process", 0 );
- doUseClock( "B,C", "process", 1 );
- doUseClock( "E", "process", 2 );
- doUseClock( "A,F", "process", 3 );
-\endverbatim
-
-Next we initialize them:
-
-\verbatim
- doReinit();
-\endverbatim
-
-During the \e doReinit call, the \e reinit function of the objects would be
-called in the following sequence:
-\verbatim
- D, B, C, E, A, F
-\endverbatim
-
-Finally, we run the calculation for 10 seconds:
-
-\verbatim
- doStart( 10 );
-\endverbatim
-
-*/
diff --git a/moose-core/Docs/developer/doxygen-design-document.cpp b/moose-core/Docs/developer/doxygen-design-document.cpp
deleted file mode 100644
index 31957ab9898e6ce098983a6cdf6dbe86f8c46c1c..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/doxygen-design-document.cpp
+++ /dev/null
@@ -1,50 +0,0 @@
-/**
-\page DesignDocument Design Document
-
-\section DD_Goals Goals
-- Cleanup.
-- Handle multithreading and MPI from the ground up.
-
-\section DD_WhyDoThis Why do this?
-It is a huge amount of work to refactor a large existing code base. This is
-needed here, and was in fact anticipated, for two reasons:
-- We needed the experience of building a fairly complete, functioning system
- to know what the underlying API must do.
-- The original parallel stuff was a hack.
-
-This redesign does a lot of things differently from the earlier MOOSE messaging.
-- Introduces a buffer-based data transfer mechanism, with a fill/empty
- cycle to replace the earlier function-call mechanism. The fill/empty
- cycle is needed for multithreading and also works better with multinode
- data traffic.
-- All Elements are now assumed to be array Elements, so indexing is built into
- messaging from the ground up.
-- Field access function specification is cleaner.
-- Separation of function specification from messaging. This means that any
- message can be used as a communication line for any function call
- between two Elements. This gives an enormous simplification to message
- design. However, it entails:
-- Runtime type-checking of message data, hopefully in a very efficient way.
- As message setup is itself runtime, and arbitrary functions can sit
- on the message channels, it turns out to be very hard to
- do complete checking at compile or setup time.
-- Wildcard info merged into messages.
-- Three-tier message manipulation hierarchy, for better introspection and
- relating to higher-level setup calls. These are
- Msg: Lowest level, manages info between two Elements e1 and e2.
- Deals with the index-level connectivity for the Element arrays.
- Conn: Mid level. Manages a set of Msgs that together make a messaging
- unit that takes a function call/data from source to a set of
- destination Elements and their array entries. Has introspection
- info. Is a MOOSE field.
- Map: High level. Manages a set of Conns that together handle a
- conceptual group. Equivalent to an anatomical projection from
- one set of neurons to another in the brain. Equivalent to what
- the 'createmap' function would generate. Has introspection.
- Is a MOOSE Element.
-
-- Field access and function calls now go through the messaging interface. Not
- necessarily the fastest way to do it, but simplifies life in a
- multinode/multithreaded system, and reduces the complexity of the
- overall interface.
-*/
diff --git a/moose-core/Docs/developer/doxygen-main.cpp b/moose-core/Docs/developer/doxygen-main.cpp
deleted file mode 100644
index 7c1d36aacd781bd4783efe45d868669a14fca7ce..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/doxygen-main.cpp
+++ /dev/null
@@ -1,48 +0,0 @@
-/**
-\mainpage MOOSE source code documentation
-
-\section intro_sec Introduction
-
-MOOSE is the base and numerical core for large, detailed simulations
-including Computational Neuroscience and Systems Biology. MOOSE spans the
-range from single molecules to subcellular networks, from single cells to
-neuronal networks, and to still larger systems. it is backwards-compatible
-with GENESIS, and forward compatible with Python and XML-based model
-definition standards like SBML and NeuroML.
-
-MOOSE uses Python as its primary scripting language. For backward
-compatibility we have a GENESIS scripting module, but this is deprecated.
-MOOSE uses Qt/OpenGL for its graphical interface. The entire GUI is
-written in Python, and the MOOSE numerical code is written in C++.
-
-\section support_sec Hardware and availability
-MOOSE runs on everything from laptops to large clusters. It supports
-multiple-core machines through threading, and cluster architectures using
-MPI, the Message Passing Interface. MOOSE is compiled for Linux,
-MacOS, and to the extent that we can get it to compile, on Windows.
-
-MOOSE is free software.
-MOOSE makes extensive use of external libraries. The main MOOSE code itself
-is LGPL, meaning it is easy to reuse with attribution but will remain
-free. However, the common release of MOOSE uses the GNU scientific library
-(GSL) which is under the GPL. For such releases, MOOSE should be treated
-as also being under the GPL.
-
-Apart from the auto-generated documentation for the source-code itself, here are
-some higher-level hand-written documents:
-
-\ref ProgrammersGuide
-
-\ref AppProgInterface
-
-\ref DesignDocument
-
-\ref HSolveDevOverview
-
-\ref HSolveImplementation
-
-\ref Profiling
-
-\ref ParamFitting
-
-*/
diff --git a/moose-core/Docs/developer/doxygen-programmers-guide.cpp b/moose-core/Docs/developer/doxygen-programmers-guide.cpp
deleted file mode 100644
index ba756f8207a8c13ecfa8e820b4f2c719d2609674..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/doxygen-programmers-guide.cpp
+++ /dev/null
@@ -1,277 +0,0 @@
-/**
-\page ProgrammersGuide Programmer's Guide
-Documentation for programmers.
-
-\section PG_ProcessLoop Process Loop
-The MOOSE main process loop coordinates script commands, multiple threads
-to execute those commands and carry out calculations, and data transfer
-between nodes.
-
-\subsection PG_Threads Threads
-MOOSE runs in multithread mode by default. MOOSE uses pthreads.
-
-1. The main thread (or the calling thread from a parser such as Python)
-is always allocated.\n
-2. MOOSE estimates the number of CPU cores and sets up that same number
-of compute threads. To override this number, the user can specify at the
-command line how many threads to use for computation.\n
-If MOOSE is running with MPI, one more thread is allocated
-for controlling MPI data transfers.
-
-MOOSE can also run in single-threaded mode. Here everything remains in the
-'main' thread or the parser thread, and no other threads are spawned.
-
-\subsection PG_ProcessLoopDetails Multithreading and the Process Loop
-The MOOSE process loop coordinates input from the main thread, such as
-parser commands, with computation and message passing. MOOSE has one
-process loop function (processEventLoop) which it calls on all compute
-threads. All these threads
-synchronize on custom-written barriers, during which a special single-
-thread function is executed.
-
-The sequence of operations for a single-node, multithread calculation is
-as follows:
-
-1. The Process calls of all the executed objects are called. This typically
- triggers all scheduled calculations, which emit various messages. As
- this is being done on multiple threads, all messages are dumped into
- individual temporary queues, one for each thread.\n
-2. The first barrier is hit. Here the swapQ function consolidates all
- the temporary queues into a single one.\n
-3. All the individual threads now work on the consolidated queue to digest
- messages directed to the objects under that thread. Possibly further
- messages will be emitted. As before these go into thread-specific
- queues.\n
-4. The second barrier is hit. Now the scheduler advances the clock by one
- tick.\n
-5. The loop cycles back.
-
-In addition to all this, the parser thread can dump calls into its special
-queue at any time. However, the parser queue operates a mutex to
-protect it during the first barrier. During the first barrier, the
-queue entries from the parser thread are also incorporated into the
-consolidated queue, and the parser queue is flushed.
-
-These steps are illustrated below:
-
-@image html MOOSE_threading.gif "MOOSE threading and Process Loop"
-
-\subsection PG_MPIProcessLoopDetails Multinode data transfer, Multithreading and the Process Loop
-MOOSE uses MPI to transfer data between nodes. The message queues are
-already in a format that can be transferred between nodes, so the main
-issue here is to coordinate the threads, the MPI, and the computation in
-a manner that is as efficient as possible.
-When carrying out MPI data transfers, things are somewhat more involved.
-Here we have to additionally coordinate data transfers between many nodes.
-This is done using an MPI loop (mpiEventLoop) which is called on
-a single additional thread. MPI needs two buffers: one for sending and
-one for receiving data. So as to keep the communications going on in
-the background, the system interleaves data transfers from each node with
-computation. The sequence of operations starts out similar to above:
-
-1. The Process calls of all the executed objects are called. This typically
- triggers all scheduled calculations, which emit various messages. As
- this is being done on multiple threads, all messages are dumped into
- individual temporary queues, one for each thread. MPI thread is idle.\n
-2. The first barrier is hit. Here the swapQ function consolidates all
- the temporary queues into a single one.\n
-3. Here, rather than digest the local consolidated queue, the system
- initiates an internode data transfer. It takes the node0 consolidated
- queue, and sends it to all other nodes using MPI_Bcast. On node 0,
- the command reads the provided buffer. On all other nodes, the command
- dumps the just-received data from node 0 to the provided buffer.
- The compute threads are idle during this phase.\n
-4. Barrier 2 is hit. Here the system swaps buffer pointers so that
- the just-received data is ready to be digested, and the other buffer
- is ready to receive the next chunk of data.\n
-5. Here the compute threads digest the data from node 0, while the
- MPI thread sends out data from node 1 to all other nodes.\n
-6. Barrier 2 comes round again, buffer pointers swap.\n
-7. Compute threads digest data from node 1, while MPI thread sends out
- data from node 2 to all other nodes.\n
-... This cycle of swap/(digest+send) is repeated for all nodes.\n
-
-8. Compute threads digest data from the last node. MPI thread is idle.\n
-9. In the final barrier, the clock tick is advanced.\n
-10. The loop cycles back.
-
-As before, the parser thread can dump data into its own queue, and this
-is synchronized during the first barrier.
-
-These steps are illustrated below:
-
-@image html MOOSE_MPI_threading.gif "MOOSE threading and Process Loop with MPI data transfers between nodes."
-
-\subsection ksolve_threading Threading with the Kinetics GSL solver.
-
-Currently we only subdivide voxels, not parts of a single large model
- within one voxel.\n
-<ul>
-<li>The GslIntegrator handles Process and Reinit. This drives the data
-structures set up by the Stoich class.
-<li>The Compartment, which is a ChemMesh subclass,
- is subdivided into a number of MeshEntries (voxels).
-<li>The GslIntegrator has to be created with as many instances as there are
-MeshEntries (voxels) in the mesh.
-<li>The setup function (currently manual) calls the GslIntegrator::stoich()
-function on all instances of GslIntegrator (e.g., using setRepeat).
-<li>The scheduling (currently manual) does:
- <ol>
- <li>Clock0: MeshEntry::process.
- <li>Clock1: GslIntegrator::process.
- </ol>
-<li>During Reinit, the GslIntegrator builds up a small data structure called
-StoichThread. This contains a pointer to the Stoich, to the ProcInfo, and
-the meshIndex. There is a separate StoichThread on each GslIntegrator
-instance.
-<li> During Process on the MeshEntry, the following sequence of calls
-ensues:
- <ol>
- <li>ChemMesh::updateDiffusion( meshIndex )
- <li>Stoich::updateDiffusion( meshIndex, stencil )
- <li>Iterate through stencils, calling Stencil::addFlux for meshIndex
- <li>In Stencil::addFlux: Add flux values to the Stoich::flux vector.
- </ol>
-
-<li>During Process on the GslIntegrator:
- <ol>
- <li> the GslIntegrators on all threads call their inner loop
- for advancing to the next timestep through gsl_odeiv_evolve_apply.
- <li>The GslIntegrators on all threads call Stoich::clearFlux.
- </ol>
-<li>During Process on the Stoich, which is called through the GslIntegrator
- functions, not directly from Process:
- <ol>
- <li>Through the GSL, Stoich::gslFunc is called on each thread. This
- calls the innerGslFunc with the appropriate meshIndex. This does the
- calculations for the specified voxel. These calculations include
- the chemistry, and also add on the appropriate flux terms for each
- molecule at this meshIndex.\n
- <li>The Stoich::clearFlux function zeroes out all the entries in the
- flux_ vector at the specified meshIndex.\n
- </ol>
-</ul>
-
-\section Solvers_zombies Solvers and Zombies
-\subsection SolversOverview Overview
-\subsection WritingZombies Writing Zombies
-Zombies are superficially identical classes to regular MOOSE classes, only
-they are now controlled by some kind of numerically optimized solver. The
-role of the Zombie is to give the illusion that the original object is there
-and behaving normally (except perhaps computing much faster). All the original
-messages and fields are preserved. It is important that there be a one-to-one
-match between the original and zombie list of Finfos in the Cinfo static
-intialization.\n
-Zombies provide an interface between the original fields and the solver. They
-usually do so by maintaining a pointer to the solver, and using its access
-functions.\n
-Zombie classes typically also provide two special functions: \n
-zombify( Element* solver, Element* orig)
-and unzombify( Element* zombie). These do what you might expect from the name.
-The solver calls these operations during setup.\n
-
-There are two main kinds of zombies:
-<ul>
- <li> Soulless zombies: These lack any data whatsoever, and are
- derived classes from the solver. The Zombie data is nothing
- but a pointer to the managing solver, and is never duplicated.
- These are managed by a ZombieHandler. During the zombify
- routine, all the relevant data goes over to the solver,
- and the original data and dataHandler is deleted.
- <li> Transformed Zombies: These carry some data of their own, as well as
- a pointer to the managing solver. If they are converted to an
- array, or resized they have to have their own data resized too.
- These are managed by a regular DataHandler. During the
- zombify routine, some parts of the data are copied over to
- the new Zombie data structure, some go to the solver, and the
- rest is discarded. The original data is deleted.
-</ul>
-
-\section NewClasses Writing new MOOSE classes
-\subsection NewClassesOverview Overview
-
-MOOSE is designed to make it easy to set up new simulation classes. This
-process is discussed in detail in this section. Briefly, the developer
-provides their favourite implementation of some simulation concept as
-a class. The functions and fields of this class are exposed to the MOOSE
-system through a stereotyped ClassInfo structure. With this, all of the
-MOOSE functionality becomes available to the new class.
-
-\subsection FunctionsOnObjects Functions on MOOSE objects
-
-MOOSE provides a general way for objects to call each other's functions through
-messaging, and for the script to also call these functions. To do this
-functions are exposed to the API in two layers. The top layer associates
-names with each function, using Finfos. A DestFinfo is the most straightforward
-way to do this, as it handles just a single function. ValueFinfos
-and their kin are associated with two functions: a set function and a get
-function.
-
-The second layer wraps each function in a consistent form so that the message
-queuing system can access it. This is done by the OpFunc and its
-derived classes, EpFunc, UpFunc, GetOpFunc, ProcOpFunc, and FieldOpFunc.
-The form of the wrapping in all cases is:
-
-\verbatim
-void op( const Eref& e, const Qinfo* q, const double* buf ) const
-\endverbatim
-
-The job of each of these classes is to then map the arguments in the buffer
-to the arguments used by the object function. Here are some of the key features:
-<ul>
- <li> OpFunc: These contain just the arguments to the function.
- For example:
- \verbatim
- OpFunc1< Foo, double >( &Foo::sum );
- ...
- void Foo::sum( double v ) {
- tot_ += v;
- }
- \endverbatim
- These are useful when the function only operates on the internal fields
- of the destination object.
-
- <li> EpFunc: These pass the Eref and the Qinfo in ahead of the other
- function arguments. This is essential when you want to know about the
- MOOSE context of the function. For example, if you need to send a
- message out you need to know the originating object and thread. If you
- want to manipulate a field on the Element (as opposed to the individual
- object), again you need a pointer to the Eref. If your function needs
- to know what the originating Object was, it can get this from the
- Qinfo. For example:
- \verbatim
- EpFunc1< Bar, double >( &Bar::sum );
- ...
- void Bar::sum( const Eref& e, const Qinfo* q, double v ) {
- tot_ += v;
- Id src = q->src();
- msg->send( e, q->threadNum(), tot_, src );
- }
- \endverbatim
-
- <li> UpFunc: These are used in FieldElements, where the actual data
- and operations have to be carried out one level up, on the parent.
- For example, Synapses may be FieldElements sitting as array entries
- on a Receptor object. Any functions coming to the Synapse have to be
- referred to the parent Receptor, with an index to identify which
- entry was called. UpFuncs do this.
- \verbatim
- static DestFinfo addSpike( "addSpike",
- "Handles arriving spike messages. Argument is timestamp",
- new UpFunc1< Receptor, double >( &Receptor::addSpike )
- );
- // Note that the DestFinfo on the Synapse refers to a function
- // defined on the Receptor.
- ...
- void Receptor::addSpike( unsigned int index, double time ) {
- Synapse& s = synTable[index];
- s.addEvent( time );
- }
- \endverbatim
-
- <li> ProcOpFunc:
- <li> GetOpFunc:
- <li> FieldOpFunc:
-</ul>
-
-*/
diff --git a/moose-core/Docs/developer/hsolve-developer-overview.cpp b/moose-core/Docs/developer/hsolve-developer-overview.cpp
deleted file mode 100644
index 898b663e3855bd51afb3d76180502ff7ca09385b..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/hsolve-developer-overview.cpp
+++ /dev/null
@@ -1,208 +0,0 @@
-/**
-
-\page HSolveDevOverview HSolve Overview
-
-\section Introduction
-
-This document gives an overview of the Hines' solver (HSolve) implementation
-in MOOSE. At present it talks more about the interaction between HSolve and
-the rest of MOOSE, and does not talk about HSolve's internals (that is, the
-numerical implementation). Hence, it will be useful for someone who is
-implementing a new numerical scheme in MOOSE.
-
-When a neuronal model is read into MOOSE (from a NeuroML file, for example),
-it is represented inside MOOSE by biophysical objects (of type Compartment,
-HHChannel, etc.) linked up by messages. Representing the model in terms of
-objects and messages is nice because it provides a natural interface that
-the user and the rest of the system can use.
-
-These objects have fields, using which the user can specify model
-parameters, and monitor state variables during a simulation. The objects
-also have some ODE solving code (usually Exponential Euler, or EE) which
-allows them to advance their own state. The messages allow the objects to
-talk to each other. In addition, the message connectivity depicts the
-model's structure.
-
-In absence of HSolve, these objects do the following things:
-- They are woken up once every time-step to perform their calculations.
- (Usually a function called process()).
-- Serve parameter and state variables via fields. For example, for plotting, a
- Compartment's Vm may be inquired once every few time-steps. Objects do this
- by providing a get() function for each field, and also a set() function to
- change the field values.
-- Communicate with each other via messages. For example, a Compartment object
- will receive axial current from its neighbouring compartments, and also
- channel current from HHChannel objects.
-- Communicate with "external" objects (e.g.: other neurons) via messages. For
- example, sending/receiving synaptic events, receiving current injection in a
- compartment, etc.
-
-This method of doing calculations is good because it is simple to implement,
-and also provides a fallback method. However, it is very slow for the following
-reasons:
-- The EE method itself is slow. Sometimes even for simple models with a 2-3
- compartments and channels, a timestep of 1e-6 seconds does not give
- accurate results. On the other hand, with HSolve, a timestep of 50e-6 is
- usually enough even for the biggest models.
-- Objects exchange information using messages. With a model of ~100 compartments
- and 2 channels per compartment, one can expect ~1000 messages being exchanged
- per time-step. This can seriously slow down calculations.
-- Objects may be spread out in memory, which will lead to a lot of cache misses.
- A single cache miss leads to a penalty of ~200-400 processor cycles.
-
-The Hines' solver, in addition to being a higher-order integration method, also
-increases speed by doing all the calculations in one place, and storing all the
-data in arrays. This eliminates messaging overheads, and improves data locality.
-
-At the same time, one will like to retain the original objects-and-messages
-representation of the model, so that the user can easily inspect and
-manipulate it. In MOOSE, this is accomplished by replacing the original
-objects with "zombie" objects, whenever a solver like the HSolve is created.
-The clients of the original objects remain unaware of this switch, and to
-them, the zombie objects look just like the originals. The zombie objects
-have the same fields as the original objects, and the message connectivity
-is also retained. The illusion is made complete by letting the zombie
-objects forward any field queries and incoming messages to the HSolve. More
-detail on zombie objects is in the "Zombies" section below.
-
-\section ConceptualOverview Conceptual Overview
-
-MOOSE allows you to keep your main numerical code very loosely coupled with
-the rest of the MOOSE system. HSolve makes good use of this, and keeps the
-numerical code as independent of MOOSE-specific concepts/classes as
-possible. The points of interaction between HSolve and the rest of MOOSE are
-neatly contained in a few classes/files.
-
-Note: At present, a single HSolve object handles calculations for a single
-neuron. Soon, HSolve will also handle calculations for arrays of identical
-neurons.
-
-Here is an overview of how things proceed chronologically in a simulation:
-
--# The user loads in a model, from, say a NeuroML file. The model is represented
- inside MOOSE as a bunch of objects, connected by messages. The objects are
- of type Compartment, HHChannel, etc. The connections between these
- objects capture the structure of the model. Each of the objects have fields
- (e.g.: "Vm" for a Compartment, "Gk" for an HHChannel). The user can use
- these fields to read/modify the parameters and state of the model.
--# The objects are capable of doing their own calculations at simulation time,
- using the Exponential Euler method. Usually, the user "schedules" all the
- objects constituting the model. This means hooking up the objects to a clock,
- which will invoke the objects at regular intervals to do their calculations.
- However, since we want HSolve to the calculations instead of the original
- objects, this scheduling step is not necessary.
--# The user connects this single-neuron model with other, external things. For
- example, a Table object may be connected to a Compartment object for the
- purpose of monitoring its Vm, later during the simulation. Other examples
- are:
- - a Table providing time-varying current-injection to a compartment.
- - synaptic connections between compartments belonging to different
- neurons.
--# The user creates an HSolve object.
--# The user "schedules" the HSolve object so that it can do its calculations.
--# The user sets the "dt" field of the HSolve object.
--# The user points the HSolve object to the model. This is done by setting
- the HSolve's "target" field to the location of model inside MOOSE.
-
- (Note: MOOSE, arranges objects in a tree, just like directories and files
- are arranged in a tree by filesystems. Hence, the location of a model is
- simply the "path" to an object which contains all of the model's objects).
-
- Setting the "target" field causes HSolve to do the following:
- -# Traverse the model, and build internal data structures based on the
- model's structure, parameters and state.
- -# "Deschedule" all the original objects, so that they are not longer
- invoked by the clock to do their calculations.
- -# Create "zombie" objects. More on this in the "Zombies" section below.
--# The user runs the simulation. As mentioned above, only the HSolve is invoked
- every time-step to do its calculations. Further, the rest of the system
- continues to interact with the individual zombified biophysical objects, not
- knowing that HSolve is doing all the thinking in the background.
-
-Note that at present, the user is responsible for carrying out all the above
-steps. In the future, a "solver manager" will be implemented which will take
-over most of the above responsibilities from the user. The user will mainly
-need to specify the choice of solver: EE, HSolve, or any other, if present.
-
-\section Zombies
-
-When an HSolve object is created, it takes over all the above functions from
-the original objects. At the same time, each of the original objects is
-replaced by a corresponding "zombie" object. For example, a Compartment
-object is replaced with a ZombieCompartment object. The user (or the rest
-of the system) continues to interact with the zombie objects, unaware of the
-switch. The role of the zombies is to act as fully-functional stand-ins,
-while letting the HSolve do all the thinking. Hence, a Table object can
-continue requesting for Vm from the compartment it was connected to, not
-knowing that the compartment has now been replaced by a zombie. Simliarly,
-another Table object can continue feeding current inject values to a
-compartment, not knowing that they are being fed into HSolve. All of this is
-accomplished in the following way:
-
-- The original objects are disconnected from the scheduling system, so that
- they are no longer woken up for performing their calculations. Instead, the
- HSolve object is invoked once every time-step.
-- When a field query is made to a zombie object, it calls set/get functions on
- the HSolve, rather than on itself.
-- Similarly, when an incoming message arrives, a function on the HSolve is
- called to handle it.
-- During a simulation, the HSolve sends out messages on behalf of the original
- objects, to any outside objects that are connect to objects belonging to the
- handled neuronal model.
-
-For further details about zombies, see the \ref ProgrammersGuide.
-
-\section code C++ code: classes and files
-
-Now we look at the different C++ classes that make up HSolve, and at the
-role they play in the processes described above.
-
-At setup time, most of the information flow is in the MOOSE --> HSolve
-direction. Here, the HSolveUtils class is of particular interest.
-
-At simulation time, most of the information flow is in the HSolve --> MOOSE
-direction. Here, the HSolve class and the Zombie classes capture most of the
-interactions.
-
-The numerical implementation is contained in the 3 classes HSolveActive,
-HSolvePassive, and HinesMatrix.
-
-Further details below:
-
--# HSolveUtils: This is a little library of convenience functions built on top
- of more basic MOOSE API calls. This library is meant for someone
- implementing a numerical scheme, and wishing to read in the model. A
- typical call looks like: "For a given compartment, give me all its
- neighbouring compartments", or, "For a given compartment, give me all the
- HHChannels that it has".
--# HSolve: The user and the rest of MOOSE interact with this class, and the
- Zombie classes. HSolve does the following:
- -# Inherits numerical code and data structures from the HSolveActive
- class.
- -# It provides an interface for looking up and modifying the parameters
- and state of the model. This is implemented as a host of set/get
- functions, written in HSolveInterface.cpp.
- -# Elevates its own status from regular C++ class to a MOOSE class. It does
- so by registering itself as a class with the MOOSE system. Here it also
- tells MOOSE that it has fields called "target" and "dt" (as mentioned
- earlier). It also specifies that it has a field called 'process', which
- allows it to be connected to a clock from the MOOSE scheduling system.
- All of this is done in HSolve::initCinfo().
- -# When the "target" field is set, it sets up its internal data structures
- using code inherited from HSolveActive. At this point, it also
- converts all the original objects into zombies.
- .
--# HSolveActive: At setup time, when the "target" field of HSolve is set,
- it triggers the HSolveActive::setup() function. This function is encoded in
- HSolveActiveSetup.cpp. It traverses the model using the HSolveUtils API,
- interrogates the model's structure, parameter and state, and sets up all the
- internal data-structures accordingly. At simulation time, HSolveActive
- does the full-fledged calculations for a neuronal model with ion channels,
- calcium, synapses, etc.The entry point for these calculations is
- HSolveActive::step().
--# HSolvePassive: This class does the compartmental calculations for passive
- neurons. Derives from HinesMatrix.
--# HinesMatrix: This class stores the HinesMatrix.
--# Zombie*: These are the zombie classes.
-
-*/
diff --git a/moose-core/Docs/developer/hsolve-implementation.cpp b/moose-core/Docs/developer/hsolve-implementation.cpp
deleted file mode 100644
index a6cbce1e11360ce9239a30cc46df8f4d429f6b90..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/hsolve-implementation.cpp
+++ /dev/null
@@ -1,156 +0,0 @@
-/**
-
-\page HSolveImplementation HSolve Implementation
-
-\section Introduction
-
-This page documents the internals of HSolve, i.e. the data structures and working of the HSolve class and its base classes. This document is meant to serve as a reference for anyone who wants to get a better understanding of how to interface with existing data structures of HSolve, or who wants to extend the existing code.
-
-\section GettingToHSolve Getting to HSolve
-
-Where are the entry points into HSolve? (from the python scripting perspective)
-
-<ol>
-
-<li>
-The first entry point is, of course, when the HSolve object is created from python, with some path. This calls the HSolve constructor, but is otherwise innocuous.
-</li>
-<br><br>
-<li>
-The second entry point, and the more important one as far as setup is concerned, is the HSolve::setup function which gets called as soon as the target field of the HSolve object (in python) is set. This is evident in the definition of the HSolve::setPath function. HSolve::setup is where the matrix for the corresponding compartment gets set up, by walking through the dendritic tree and collecting the various compartment elements. Following this, the fields of HSolveActive get populated, such as the HHChannels, gates, Calcium-dependent channels and synapses. Lastly, outgoing messages are redirected as required. The setup process will be elaborated upon shortly.
-</li>
-<br><br>
-<li>
-The third entry point is the moose.reinit() call, which automatically calls a series of reinit functions within hsolve, starting with HSolve::reinit. The reinit call basically resets the simulation to start from the beginning (all updated values are discarded and values are reinitialized). The various calls from reinit are once again explained in detail further below.
-</li>
-<br><br>
-<li>
-The last entry point, and where the actual work starts is moose.start( sim_dt ), which triggers the calling of HSolveActive::step (via HSolve::process) repeatedly. This is where the actual simulation happens.
-</li>
-<br><br>
-
-</ol>
-
-\section HSolveMembers HSolve classes and members
-
-\subsection HinesMatrixSetup Hines Matrix Setup and Data Members
-
-For setup, I'm going to take a bottom-up approach, and start with the Hines Matrix itself: how it is organized as a data structure and how it is accessed in the HSolve code. In order to do this, I'm first going to talk about the Hines method itself.
-
-- The Hines Matrix itself is an admittance matrix of the dendritic tree, after the Ek and Gk values of the various channels have been calculated at a given time step. (TODO: explain half-time step at which each operation is performed)
-
-- The Hines Matrix is a predominantly tridiagonal matrix, with off-tridiagonal elements appearing only when there are branches (or junctions) in the dendritic tree. This is ensured by the indexing mechanism:
- - The Hines indexing mechanism starts from a leaf and performs a depth-first-search on the tree.
- - Numbers are assigned "on the way up", after having exhausted all children of a particular node.
- - The position of the soma is not relevant to the indexing scheme.
-
-- Each compartment in the tree contributes to the diagonal of the Hines Matrix. Neighbouring compartments will contribute to corresponding cells in the tridiagonal: for example, consider compartments 2-3-4 to be a linear segment in the tree. Then, compartment 3 will contribute to the diagonal element (3, 3), to elements (3, 2) and (2, 3) by virtue of its being connected to compartment 2, and to elements (3, 4) and (4, 3) by virtue of its connection with compartment 4.
-
-- Each branch in the tree is a Y-network. Consider:
- \verbatim
- 2 6
- \ /
- Y
- |
- 7 \endverbatim
- This can equivaltently be converted into the corresponding delta:
- \verbatim
- 2---6
- \ /
- 7 \endverbatim
- Therefore, a Y branch contributes three elements to each of the upper and lower halves of the triangle, 6 elements in total. In this example, these elements are (2,6) and (6,2); (2,7) and (7,2); (6,7) and (7,6). Note that because of the Hines indexing scheme, at least one of these elements will always be a part of the tridiagonal itself. Also, if we designate "parents" and "children" in the process of performing the DFS, then parents will always have a Hines index that is one more than its that of its greatest child.
-
-- Each multi-way branch is more than a Y-network. For a three-way branch, one can create upto six different branches in the equivalent "delta" configuration:
- \verbatim
- 2 4 6
- \ | /
- \|/
- Y
- |
- 7 \endverbatim
- Which becomes:
- \verbatim
- 4
- /|\
- / | \
- 2--|--6
- \ | /
- \|/
- 7 \endverbatim
- In such a scenario, the resulting electrical network has 6 unknowns (or in general nC2 unknowns, where n is the total number of nodes in the group of compartments involed at the junction). On the other hand, there are only four (or in general, n) constraints: for a given set of node voltages, the node currents must be the same before and after the transformation (or vice versa). The system of equations is therefore underconstrained. However, for the purpose of effecting the transformation, any one solution is sufficient. It can be inferred from inspection upon writing out the respective equations, that the following value of Gij satisfies the constraints:
- \verbatim Gij = Gi * Gj / Gsum \endverbatim
- where Gsum is the sum over all Gi.
-
-- The admittances produced by each compartment due to itself and its linear neighbours is stored in the HinesMatrix::HS_ vector. HS_ is a vector of doubles, consisting of the flattened diagonal and the values against which the Hines matrix is to be inverted (i.e., the external currents). HS_ can be regarded as the flattened version of an Nx4 matrix "Hines", where N is the number of compartments in the neuron.
- - Hines[i][0] (or HS_[ 4*i + 0 ]) contains the diagonal element, after including the effects of external currents.
- - Hines[i][1] contains the element to the right and bottom of Hines[i][0] in the symmetric matrix: element (i,i+1) = element (i+1,i).
- - Hines[i][2] contains the diagonal element due to passive effects alone.
- - Hines[i][3] contains the total external current injected into this compartment.
-
-- The admittances produced at junctions are stored in the HinesMatrix::HJ_ vector. HJ_ is a flattened vector comprising of elements produced by Wyes converted to Deltas. So, in the previous example, HJ_ would store (in that order) Hines[2][6], Hines[6][2], Hines[2][7], Hines[7][2], Hines[6][7], Hines[7][6]. However, the HJ_ vector itself does not store any information regarding the location of its elements within the Hines matrix.
-
-- The information linking the junctions to HJ_ is stored separately in HinesMatrix::junction_ and HinesMatrix::operandBase_ . But in order to understand these, we first need to look at how they were made. This utilizes two further data structures: HinesMatrix::coupled_ and HinesMatrix::groupNumber_ .
- - HinesMatrix::coupled_ is a vector of groups. A group is a vector of unsigned ints. There are as many groups as there are branch-points in the dendritic tree, and each group holds the children (in order of Hines index) followed by the parent. In other words, the group contains a vector of the Hines indices of all compartments surrounding a branch point, in order of Hines index. coupled_ is a vector of all such groups (one for each branch-point).
- - HinesMatrix::groupNumber_ is a map of unsigned ints to unsigned ints. Given the Hines index of a compartment (which is part of a group in coupled_), it tells you the index of its corresponding group into the coupled_ vector. That is, if i is the Hines index of a compartment, then the group it belongs to is coupled_[ groupNumber_[ i ] ].
- - HinesMatrix::junction_ is a vector of JunctionStruct. There is one element in the junction_ vector for each parent-child pair in the dendritic tree. Each element contains the Hines index of the corresponding child compartment, and a rank which denotes the number of compartments <strong>remaining</strong> in its group. "Remaining" here means the number of compartments with Hines index greater than the current compartment itself. The rank therefore tells you how many more elements of the Hines Matrix can be eliminated by this compartment.
- - HinesMatrix::operandBase_ is a map from unsigned ints to an iterator into HJ_. Given the Hines index of a compartment in a group, it gives you the iterator into HJ_ at the point corresponding to where that compartment's eliminates start. "Compartment's eliminates" here refers to the elements that must be eliminated by this compartment. In the above example of the Y branch, operandBase_[2] would point to the element corresponding to (2,6). operandBase_[6] would point to the element in HJ_ corresponding to (6,7). 7 will not be an available index in operandBase_, because there is nothing left to eliminate.
-
-- The way to iterate through HinesMatrix::HJ_, therefore, involves doing the following:
- - Iterate through HinesMatrix::junction_
- - Find the Hines index of the compartment corresponding to this JunctionStruct element.
- - Find the pointer into HJ_ using HinesMatrix::operandBase_ [ index ].
- - Find the rank (the number of elements to be eliminated by this compartment) from the JunctionStruct.
- - Move rank steps forward in HJ_.
- - Repeat.
-
-- In case you want to find the group associated with a certain compartment (for knowing the Vm values of neighbouring compartments, for, instance), then find the group as \verbatim group = coupled_[ groupNumber_[ index ] ] \endverbatim
-
-There are a few more data members of the HinesMatrix class that have not yet been discussed. These are:
-- nCompt_: the number of compartments
-- dt_: the simulation time step
-- VMid_: the voltage values of the compartments (in order of Hines index) at the middle of the time step (t + dt/2).
-- operand_: A vector of iterators into HS_, HJ_ and VMid_, which enables easy access to the relevant data during forward elimination.
-- backOperand_: A vector of iterators into HJ_ and VMid_, which enables easy access to the relevant data during backward substitution.
-- stage_: A variable that represents which of updateMatrix, backwardSubstitution and forwardElimination have been completed.
-
-\subsection HSolvePassiveSetup HSolvePassive methods
-
-HSolvePassive has methods that enable it to build up the compartment network of the neuron by inspecting the messaging strucutre. A path into the compartment network has to be supplied for each neuron. The building of the tree is accomplished by the following three methods:
-- HSolvePassive::walkTree
- This fucntion takes a valid compartment Id as input and traverses the message strucutre until a terminal compartment is found. At this point, it performs a depth-first-search with this terminal compartment as the root. Having accumulated all compartments while going down the tree in a vector (compartmentId_), the method reverses the vector so that compartments get automatically arranged in the order of their Hines indices.
-- HSolvePassive::initialize
- Initialize pulls out the membrane parameters from each of the compartments: Vm, Cm, Em, Rm and inject. All leakage channels are iterated through, and the effective Em/Rm and Cm/dt are stored in a CompartmentStruct object for each compartment.
-- HSolvePassive::storeTree
- This last method actually creates the tree object by going through compartmentId_ once again and storing the initVm, Cm, Em, Rm and Ra values in the tree_ data structure.
-
-Once the tree has been setup, it is given as a parameter to HinesMatrix which then creates the matrix out of it.
-
-HSolvePassive also contains methods to perform integration in a single-time step (backward Euler). This comprises the stages of Gaussian elimination:
-- HSolvePassive::updateMatrix
- This method is used to update matrix parameters, subject to changed compartment parameters - Em/Rm, Cm/dt and inject values.
- (Note that this function is not used. HSolveActive::udpateMatrix does everything that this function does, and a bit more)
-- HSolvePassive::forwardEliminate
- This function mostly relies on the operand_ structure created at the HinesMatrix level and uses the operands to reduce the matrix to an upper triangular matrix.
-- HSolvePassive::backwardSubstitute
- This function solves the matrix equation for the unknown VMid vector by performing a backward substitution process.
-
-\subsection HSolveActiveSetup HSolveActive setup and data members
-
- HSolveActive inherits from HinesMatrix via HSolvePassive. While HinesMatrix has methods to build up the matrix and HSolvePassive has methods to solve the matrix, HSolveActive has data and methods that allow it to manipulate channels. The three key methods involved are:
-- HSolveActive::advanceChannels
- This function recomputes the "state" values of each of the channels. The state_variable is a flattened vector of the fraction of opened gates across all channels across all compartments. To update state values, the values of rate constants are looked up from the lookup tables, depending upon what the membrane voltage and calcium concetration are at this instant.
-- HSolveActive::calculateChannelCurrents
- This function is used to re-compute the total current entering each compartment from "state" information. The state values are raised to the required power and multipled with the respective Gbar.
-- HSolveActive::advanceCalcium
- - This method pushes forward the caActivation values (total calcium current flowing into each pool) by adding up the contributions from each channel feeding the respective pools.
- - It also updates the calcium conentration in each pool depending upon the calcium current so calculated.
-- HSolveActive::updateMatrix
- - This method supersedes HSolvePassive::updateMatrix.
- - Changes in the channel conductances only affect the diagonal values of the Hines matrix (because the channel conductances connect Vm to ground). updateMatrix computes the new values of the diagonal parameters as well as the modified values of the "B" vector - the vector against which the Hines matrix is being inverted.
- - The values of inject are also modified, since injectVarying (obtained via a message) could have changed.
- - Finally, external currents, from channels not handled by HSolve, are added to the "B" vector part of HS_.
-
-
-
-
-*/
diff --git a/moose-core/Docs/developer/parameter_fitting.cpp b/moose-core/Docs/developer/parameter_fitting.cpp
deleted file mode 100644
index 9c59d499e14cab4dce2e6632df7bc3869149da8a..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/parameter_fitting.cpp
+++ /dev/null
@@ -1,120 +0,0 @@
-/**
-
-\page ParamFitting Parameter fitting
-
-\section Introduction
-
-When you have experimental data on a phenomenon, and you intend to create a computational model of it, usually you need to apply parameter fitting/searching techniques. These methods help you determine those parameters of your model that you have no reference on. Parameter fitting using MOOSE models are accomplished through utilizing <a target="_blank" href="http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00063/full">Optimizer</a> <a href="#cite1">[1]</a>, a parameter fitting tool developed for neural simulations.
-
-
-\section Installation Installation
-
-Installation of Optimizer and it's dependencies can be done by running through the <a target="_blank" href="http://optimizer.readthedocs.org/en/latest/install.html">Optimizer documentation</a>. If MOOSE is already installed, dependencies like inspyred, wxpython and pyelectro are needed to installed only besides Optimizer.
-
-If you encounter errors while simulating, then probably the repository of Optimizer is not updated by some changes I made. Here is the repository of a definitely <a href="https://github.com/csiki/optimizer" target="_blank">working (but not necessarily the latest) version</a>.
-
-
-\section Usage Usage
-
-The <a target="_blank" href="http://optimizer.readthedocs.org/en/latest/tutorial.html">tutorial</a> of Optimizer can guide you through how to work with the GUI, though it's usage is quite obvious.
-
-So the process of parameter fitting consists of the following steps:
-
-<ol>
- <li>Provide experimental data, simulation script, fitting settings to Optimizer,</li>
- <li>Run parameter fitting,</li>
- <ol>
- <li>Optimizer provides parameters to the simulation through params.param file located next to the simulation script,</li>
- <li>Optimizer runs the simulation,</li>
- <ol>
- <li>Simulation retrieves the parameters from params.param using OptimizerInterface,</li>
- <li>Simulation runs with the given parameters,</li>
- <li>Simulation saves the results to trace.dat, located next to the simulation script, using OptimizerInterface,</li>
- </ol>
- <li>Optimizer compares the results with the experimental data, finishes if the results ~fit the experimental data, otherwise goes to 2.1 to run the simulation again with other parameters.</li>
- </ol>
- <li>Optimizer shows parameter fitting results.</li>
-</ol>
-
-Let's see an example of a cooperation between Optimizer and MOOSE. First create a python script that is going to be the simulation file, in which your MOOSE code would be that runs the simulation. Let's call it opttest.py:
-
-\verbatim
-
-from moose import optimizer_interface
-import math
-
-# constants
-time_range = 1000 # time range (let's say in ms)
-experimental_params = [2.1, 3.5, 8.1] # these should be retrieved at the
- # end of the parameter fitting
-
-def simulation(t, params):
- """
- Our simple, artificial 'neural simulation'.
- """
- return math.exp(-params[0]*t) * params[1] + params[2] * (t/5) * 0.1
-
-def generateInput():
- """
- Generates the input file using the 'experimental parameters'.
- """
- with open('input.dat', 'w') as f:
- for t in range(time_range):
- f.write(str(simulation(t, experimental_params)) + '\n')
-
-#~ generateInput() # this should be uncommented at the first time
-#~ # to generate the experimental data of the simulation
-
-# generally when you put up your MOOSE simulation, everything before this
-# comment is NOT needed
-# load params
-oi = optimizer_interface.OptimizerInterface() # load parameters from params.param
-params = oi.getParams() # stores the parameters as a list of floats
-
-# simulate using simulation() function
-results = []
-for t in range(time_range):
- results.append(simulation(t, params))
-
-# add & write traces
-oi.addTrace(results) # adds a trace as the result of the simulation
-oi.writeTraces() # writes the added traces to trace.dat so
- # Optimizer can read and compare them to the
- # experimental data
-
-\endverbatim
-
-Instead of having a real MOOSE simulation, there's just an artificial one (basically a function) implemented - it is faster to run, and fundamentally the same as if we had a real MOOSE simulation.
-
-At first we have some global constants and two functions to simplify the code. The main part can be found after the OptimizerInterface object is initialised. We retrieve the parameters that Optimizer has suggested, then we run the 'simulation' with these parameters. Next we add a trace of the simulation's output that is going to be compared with the experimental data. Here you can either pass an iterable object (like a simple python list or numpy.array), or a moose.Table object. At the end we write the trace to trace.dat.
-
-To use this script, first uncomment the call to generateInput() function so it can save the 'experimental data' into input.dat. This input may contain the times (not necessary) of the sampling in the first column and each trace in another following column. Run the script then comment generateInput() back - not necessary, but it would slow down the simulation. After that, open Optimizer GUI by running neuraloptimizer file inside optimizer_base_dir/optimizer/. Select input.dat as your input file, with the following parameters (and also uncheck 'Contains time'):
-<ul>
- <li>number of traces: 1</li>
- <li>length of traces (ms): 1000</li>
- <li>sampling frequency (Hz): 1000</li>
-</ul>
-
-Then click the Load trace button and if everything goes well, you should see a plot of your input data (now a linear function). Click the arrow at the top!
-
-On the second layer select 'external' where originally Neuron is selected. It tells Optimizer that we'd like to use a simulator apart from Neuron. Then in the 'Command to external simulator' box three elements should be given separated by space:
-<ul>
- <li>the command to execute: python - this will run our python script (obviously) consisting the model definition and running of simulation (opttest.py)</li>
- <li>the model file: /absolute_path_to_the_model_file/opttest.py</li>
- <li>(some options passed to your simulation script as commandline arguments)</li>
- <li>number of parameters to optimize: 3</li>
-</ul>
-So the whole command should look somewhat like this:
-\verbatim python /absolute_path_to_the_model_file/opttest.py 3 \endverbatim
-
-On the next layer you can select the fitness function(s) of your choice. Let's select MSE, with a weight of 1.0.
-
-On the 'Select Algorithm' layer choose Simulated Annealing (it's fast enough), then choose the boundaries and the starting points of your parameters (take into consideration the experimental parameters in opttest.py). After that, you can run the parameter fitting, leaving the rest settings as default.
-
-When the parameter search is finished you can save the proper parameter values, see how the model fits the experimental data or check MSE values evolve simulation after simulation.
-
-\author Viktor Tóth
-
-<p><a name="cite1">[1] P. Friedrich, M. Vella, A. I. Gulyás, T. F. Freund, and S. Káli, “A flexible, interactive software tool for fitting the parameters of neuronal models,†Front. Neuroinform, vol. 8, p. 63, 2014.</a></p>
-
-*/
diff --git a/moose-core/Docs/developer/profiling.cpp b/moose-core/Docs/developer/profiling.cpp
deleted file mode 100644
index 4a7c9ed0896cb5ad6c30fa59953f6faebd9472ba..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/profiling.cpp
+++ /dev/null
@@ -1,135 +0,0 @@
-/**
-
-\page Profiling Profiling
-
-\section Introduction
-
-It is possible to do profiling without altering any C++ implementation, and without writing any C++ testbed. Using Google's <a target="_blank" href="https://code.google.com/p/gperftools/">gperftools</a> combined with <a href="http://cython.org/">cython</a>, you can do C++ profiling by writing python script running the MOOSE functions in quetion.
-
-First cython, gperftools, libc6-prof packages have to be installed. Secondly a cython wrapper should be made for three functions of gperftools. After that, moose may be recompiled with the 'profile' option. Lastly, the wrapper may be included into arbitrary python script, thus gperftools functions can be used.
-
-\section PackageInstalltion Package Installation
-
-<ul>
-<li>Cython: \verbatim ~$ sudo apt-get install cython \endverbatim</li>
-
-<li>gperftools: download it from <a target="_blank" href="https://code.google.com/p/gperftools/downloads/list">here</a>, then install it.</li>
-
-<li>libc6-prof: \verbatim ~$ sudo apt-get install libc6-prof \endverbatim</li>
-
-<li>kcachegrind (optional, for interpreting profiler output): \verbatim ~$ sudo apt-get install kcachegrind \endverbatim</li>
-
-</ul>
-
-\section CythonWrapper Cython gperftools wrapper
-
-The simplest way to get the wrapper done is to write a cython script wrapping the gperftools functions and a python script that compiles the wrapped functions and link them to the gperftools library.
-
-Let's call the cython script gperftools_wrapped.pyx:
-
-\verbatim
-
-cdef extern from "gperftools/profiler.h":
- int ProfilerStart(char* fname)
- void ProfilerStop()
- void ProfilerFlush()
-
-def ProfStart(fname):
- return ProfilerStart(fname)
-
-def ProfStop():
- ProfilerStop()
-
-def ProfFlush():
- ProfilerFlush()
-
-\endverbatim
-
-Here we define a python function for each function of gperftools that we wrap. More functions can be wrapped for more custom profiling (see ProfilerStartWithOptions()).
-
-The python compiler script may look something like this (setup.py):
-
-\verbatim
-
-from distutils.core import setup
-from Cython.Build import cythonize
-
-setup(
- name = 'gperftools_wrapped',
- ext_modules = cythonize("gperftools_wrapped.pyx"),
-)
-
-\endverbatim
-
-Now the setup.py may be run with the following manner, adding the -lprofiler flag:
-\verbatim ~$ python setup.py build_ext --inplace -lprofiler \endverbatim
-
-If everything went right now you should have gperftools_wrapped.c, gperftools_wrapped.so, and a build directory as result of the compilation.
-
-Put gperftools_wrapped.so nearby your python testbed and import as gperftools_wrapped, so you can profile python C extensions. But (!) first the C extensions may be compiled using the -lprofiler flag.
-
-\section MooseRecomp Moose recompilation
-
-To profile moose, it should be recompiled with altering the Makefile setting BUILD: \verbatim BUILD=profile \endverbatim
-
-Essentially you should add the -lprofiler flag. So if the flags corresponding to the "profile" BUILD option does not include -lprofiler you should add it yourself (probably that is the case).
-
-Flags to use for example: \verbatim CXXFLAGS = -pg -lprofiler -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DUSE_GENESIS_PARSER \endverbatim
-
-You may only add the -lprofiler flag to the Makefile which compiles the C++ code you are interested in profiling (not tested). Then recompile moose.
-
-\section ProfilingInAction Profiling in action
-
-Before profiling one should always set the PYTHONPATH to the directory from where python picks up moose functions. To get the function names in your profiling, this should be done, whether it is already set in e.g. your .bashrc script. Example:
-
-\verbatim export PYTHONPATH=/path_to_moose/python/ \endverbatim
-
-To test profiling let's use an existing demo to check the runtime of HSolve functions.
-
-From the moose directory alter the script at Demos/traub_2005/py/test_hsolve_tcr.py. First import the wrapper we just made.
-
-\verbatim from gperftools_wrapped import * \endverbatim
-
-Then edit the testHSolve function, adding the wrapper functions:
-
-\verbatim
-
- def testHSolve(self):
- ProfStart("hsolve.prof")
- self.schedule(simdt, plotdt, 'hsolve')
- self.runsim(simtime, pulsearray=pulsearray)
- self.savedata()
- ProfFlush()
- ProfStop()
-
- def testEE(self):
- pass
- #self.schedule(simdt, plotdt, 'ee')
- #self.runsim(simtime, pulsearray=pulsearray)
- #self.savedata()
-
-\endverbatim
-
-You can also comment out the testEE() function so the it will run faster.
-
-After running the python script you should have a file named hsolve.prof. As you can see the string passed to ProfStart() determines the name of the profiler's output.
-
-You can interpret the output using pprof, or if you installed kcachegrind. Note that for the 'program' parameter of pprof you should provide the _moose.so file inside /path_to_moose/python/moose/.
-
-pprof text method:
-
-\verbatim
-~$ pprof --text /path_to_moose/python/moose/_moose.so hsolve.prof > log
-~$ less log
-\endverbatim
-
-kcachegrind method:
-
-\verbatim
-~$ pprof --callgrind /path_to_moose/python/moose/_moose.so hsolve.prof > output.callgrind
-~$ kcachegrind output.callgrind
-\endverbatim
-
-\author Viktor Tóth
-
-*/
diff --git a/moose-core/Docs/developer/setget.txt b/moose-core/Docs/developer/setget.txt
deleted file mode 100644
index c4afddab9c3218011c0c12b9ae0a535d3d33ab92..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/setget.txt
+++ /dev/null
@@ -1,112 +0,0 @@
-Current system:
- - Shell::doOp
- initAck
- op.send
- while isAckPending {
- clearQ
- }
-- set
- SetGet<type>::set(const Eref& dest, const string& field, A arg)
- checkSet
- type conversions into a temp char* buffer
- Shell::dispatchSet
- Puts stuff into a prepacked buffer
- Shell::innerDispatchSet
- requestSet.send() to the target shell.
- ..........................................................
- Shell::handleSet on target shell
- Checks if prepacked buffer is single arg or vec
- if single:
- create AssignmentMsg and tie to target
- lowLevelSetGet.send() data from node 0 only.
- ..........................................................
- AssignmentMsg::exec (on all nodes and all threads)
- Checks direction
- extract prepacked buffer from arg
- Checks isDataHere and p->execThread to see if to operate
- executes op func.
- If thread 0, sends back ack.
- backward direction is similar, but does not send ack.
- ..........................................................
-
-- setVec
- SetGet< type >::setVec( const Eref& dest, const string& field,
- const vector< A >& arg )
- checkSet
- type conversions into a prepacked buffer
- Shell::dispatchSetVec
- Stuff is already in prepacked buffer
- Shell::innerDispatchSet // Note that this also deals with set.
- requestSet.send() to the target shell.
- ..........................................................
- Shell::handleSet on target shell
- Checks if prepacked buffer is single arg or vec
- if vec:
- create AssignVecMsg and tie to target
- lowLevelSetGet.send() data from node 0 only.
- ..........................................................
- AssignVecMsg::exec (on all nodes and all threads)
- Checks direction
- extracts prepacked buffer from char* arg
- Finds opFunc
- DataHandler::iterator to go through all objects
- Checks p->execThread to see if to operate
- executes op func.
- If thread 0, sends back ack.
- backward direction is a single msg and looks OK, but no ack
- ..........................................................
-
-- get
- Field< type >::get (derived from SetGet1< type > )
- Shell::dispatchGet (Blocking call).
- Find field, type checks.
- Find appropriate GetOpFunc and pass its fid
- innerDispatchGet(sheller, tgt, fid)
- initAck
- requestGet.send
- while isAckPending
- clearQ
- When data comes back into Shell::getBuf_ the isAckPending
- clears.
- Then, from within Field< Type >::get continue with:
- take ptr to returned getBuf
- Convert it
- return converted value.
- ..........................................................
- Shell::handleGet
- make new AssignmentMsg and tie to target
- lowLevelGet.send
- ..........................................................
- AssignmentMsg::exec (on all nodes and all threads)
- Checks direction
- Checks isDataHere and p->execThread to see if to operate
- executes GetOp func.
- If thread 0, sends back ack.
- backward direction is similar, but does not send ack.
- ..........................................................
- GetOpFunc::op ( defined as a template in OpFunc.h and friends)
- Gets data from object
- Converts to buffer
- fieldOp on buffer (from OpFunc.cpp)
- Puts data into prepacked buffer
- Finds incoming Msg
- Synthesizes return Qinfo
- Adds return to Q going to shell
- ..........................................................
- Shell::recvGet( PrepackedBuffer pb)
- Called with the return value put into the Q by GetOpFunc
- Sets Shell::getBuf_ size for return value
- copy return value from PrepackedBuffer into
- Shell::getBuf_
- ..........................................................
- handleAck: Adds another to the returned acks
- Eventually all the acks are back and isAckPending clears
- innerDispatchGet returns the getBuf
- ..........................................................
-
-- getVec:
- Almost identical to get, and uses most of the same functions. Only
- difference is that the handleGet sets up AssignVecMsg instead;
- and the returned arguments are placed by index into the return
- vector in recvGet.
-
diff --git a/moose-core/Docs/developer/the-messaging-system.cpp b/moose-core/Docs/developer/the-messaging-system.cpp
deleted file mode 100644
index bef52d56de9a878cc3fab8eabbf54ddef00a8025..0000000000000000000000000000000000000000
--- a/moose-core/Docs/developer/the-messaging-system.cpp
+++ /dev/null
@@ -1,171 +0,0 @@
-/**
- * \page messagingSystem The Messaging System
- *
- * \section Intro Introduction
- *
- * The messaging system is central to the way moose works. Any understanding
- * of the internals of moose must start with the messaging framework.
- *
- * The framework essentially allows "moose objects" to "send" messages to or
- * "receive" messages from each other. The following sections expand on the
- * exact implementation of sending and receiving messages, both from a C++
- * programmer's perspective as well as from a python programmer's perspective.
- *
- * (TODO: add more messaging system philosophy)
- *
- * \section mooseObjects Moose Objects
- *
- * A moose object is an instance of a moose class. A moose class is a C++ class
- * that has a Cinfo object representing it. Cinfo objects are class
- * descriptors. They describe the fields that classes want to expose in the
- * python script in one way or another.
- *
- * The fields that go into python are of three main types:
- * - Value fields: the sort that are like a simple variable that can be
- * changed as and when desired - a "public" data element on a python class
- * - Source fields: A source of messages. These fields can be used to send
- * data to other moose objects
- * - Destination fields: A destination for messages. These are fields that act
- * as recepients of messages sent by source fields.
- *
- * In an ordinary C++ class, there is no distinction between different class
- * members. In order to create the aforementioned classification of class
- * members into various field types, there is a need to use Finfo objects: the
- * so-called "field descriptors".
- *
- * Consider the example of the simple class, Example:
- *
- * \verbatim
- class Example {
-
- private:
- int x_;
-
- public:
-
- int getX() { return x_; }
- void setX( int x ) { x_ = x; }
-
- static const Cinfo *initCinfo() {
- static ValueFinfo< Example, int > x(
- "x",
- "An example field of an example class",
- &Example::getX,
- &Example::setX
- );
- static Finfo *exampleFinfos[] = { &x };
- static Cinfo exampleCinfo(
- "Example", // The name of the class in python
- Neutral::initCinfo(), // TODO
- exampleFinfos, // The array of Finfos created above
- 1, // The number of Finfos
- new Dinfo< Example >() // The class Example itself (FIXME ?)
- }
-
- }; \endverbatim
- *
- * Example shows you how you can create a value field. The initCinfo function
- * here could have been called anything. It merely does the job of creating a
- * Cinfo object for the class. This is typically the case throughout moose. The
- * ValueFinfo object takes the class and the value's data type as template
- * arguments, as shown. The initialization parameters are the name of the
- * class member in python, the python docstring for the member and the
- * addresses of the set and get functions used to access and modify the said
- * value field.
- *
- * But this alone is not enough. We have not yet created a Cinfo *object*
- * corresponding to this class. The Cinfo object can be created in any of the
- * files in the project, but it is usually created below the respective
- * initCinfo function's definition. In this case, the object would be
- * instantiated in a manner such as:
- * \verbatim
- static const Cinfo *exampleCinfo = Example::Cinfo(); \endverbatim
- *
- * This creates a Cinfo object in the same file which is picked up by pymoose
- * during compilation. Example is then made into an actual python class,
- * accessible as moose.Example (provided that the directory under which these
- * files are located is included in the main moose Makefile for compilation).
- *
- * Note the importance of the "static" storage class specifier throughout this
- * example.
- *
- * Any class that has such a Cinfo object described after it is considered to
- * have been upgraded from a C++ class into a moose class.
- *
- * It helps to have moose classes rather than C++ classes, because they
- * provide a mechanism for introspection. For example, you can "ask" a moose
- * object what its fields are. In fact, you can be even more specific and ask
- * it to tell you only its value fields, source fields or destination fields.
- *
- * \section sendingAndReceiving Sending and receiving
- *
- * Sending and receiving messages in moose is accomplished through source and
- * destination fields respectively. Once again, in order to designate a field
- * as a source or destination field, it is necessary to use an Finfo object.
- *
- * The trials directory in the moose buildQ branch gives an excellent example
- * of how to define simple source and destination Finfos.
- *
- * \verbatim
- static SrcFinfo1< double > XOut( "XOut", "Value of random field X" );
- static DestFinfo handleX( "handleX",
- "Prints out X as and when it is received",
- new OpFunc1< Receiver, double >( &Receiver::handleX )
- ); \endverbatim
- *
- * The source Finfo is defined within a function that returns the address of
- * the Finfo. This is done because the same function is called in order to use
- * the send() method of the source Finfo that activates the sending of the
- * message.
- *
- * Notice that the source Finfo is defined using the class "SrcFinfo1". The 1
- * indicates the number of variables being sent across. It is also the number
- * of template arguments that have to be supplied and the number of extra
- * parameters that go into the send() call. Sender::process() calls
- * XOut()->send( e, pthreadIndexInGroup, X_ ). The X_ here is the variable
- * being sent across. There's only one variable being sent, which is why we
- * use an SrcFinfo1. For another example, one can take a look at
- * biophysics/Compartment.cpp. Here, we need to send out two variables, so we
- * use an SrcFinfo2 class. The sending function is defined as
- * raxialOut()->send( e, pthreadIndexInGroup, Ra_, Vm_ ) to send out Ra_ and
- * Vm_. In such a manner, upto six variables can be sent out in a single
- * message.
- *
- * The destination field is defined by a handler function which is held by the
- * OpFunc class. The handler should be able to take as many variables as the
- * source field sends out. So OpFunc can also take upto six template arguments.
- * The actual handler function (be it handleX or handleRaxial) takes these many
- * values as arguments (in the same order).
- *
- * More information regarding OpFunc-like classes can be found in the
- * Programmers Guide.
- *
- * \section creatingConnections Creating connections
- *
- * So far we have taken a look at how sources and destinations are made, but
- * not at how they are actually connected. There is as yet no information
- * designating which destinations a source field is supposed to send messages
- * to when their send() method is called.
- *
- * In order to find out more about how connections are made (and also about how
- * pymoose can be used) read the pymoose walkthrough in the user documentation.
- * In the trials example, we created the connection in test_trials.py with:
- * \verbatim
- conn = moose.connect(s, 'XOut', r, 'handleX') \endverbatim
- * In order to accomplish this in C++, one would do something like:
- * \verbatim
- MsgId mid = shell->doAddMsg("Single", srcId, "XOut", destId,
- "handleX" ); \endverbatim
- * This requires the definition of a shell variable which handles the creation
- * of paths in the moose system. Read the Application Programming Interface
- * guide for more information on paths. For now, try to digest the fact that
- * the following lines create a shell object that can be used to make objects
- * on paths - a neutral object and a compartment object have been created as a
- * demonstration.
- * \verbatim
- Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
- Id n = shell->doCreate( "Neutral", Id(), "n" );
- Id c = shell->doCreate( "Compartment", n, "c" ); \endverbatim
- * This creates a Neutral object at /n and a Compartment object at /n/c/.
- *
- */
diff --git a/moose-core/Docs/doxygen/Doxyfile b/moose-core/Docs/doxygen/Doxyfile
deleted file mode 100644
index 887f36775c2afe71a1f0773e3f2543e8a71d9746..0000000000000000000000000000000000000000
--- a/moose-core/Docs/doxygen/Doxyfile
+++ /dev/null
@@ -1,2411 +0,0 @@
-# Doxyfile 1.8.9.1
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project.
-#
-# All text after a double hash (##) is considered a comment and is placed in
-# front of the TAG it is preceding.
-#
-# All text after a single hash (#) is considered a comment and will be ignored.
-# The format is:
-# TAG = value [value, ...]
-# For lists, items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (\" \").
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-
-# This tag specifies the encoding used for all characters in the config file
-# that follow. The default is UTF-8 which is also the encoding used for all text
-# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
-# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
-# for the list of possible encodings.
-# The default value is: UTF-8.
-
-DOXYFILE_ENCODING = UTF-8
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
-# double-quotes, unless you are using Doxywizard) that should identify the
-# project for which the documentation is generated. This name is used in the
-# title of most generated pages and in a few other places.
-# The default value is: My Project.
-
-PROJECT_NAME = "MOOSE - Multiscale Object Oriented Simulation Environment"
-
-# The PROJECT_NUMBER
-# could be handy for archiving the generated documentation or if some version
-# control system is used.
-
-PROJECT_NUMBER =
-
-# Using the PROJECT_BRIEF tag one can provide an optional one line description
-# for a project that appears at the top of each page and should give viewer a
-# quick idea about the purpose of the project. Keep the description short.
-
-PROJECT_BRIEF =
-
-# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
-# in the documentation. The maximum height of the logo should not exceed 55
-# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
-# the logo to the output directory.
-
-PROJECT_LOGO = moose_log.png
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
-# into which the generated documentation will be written. If a relative path is
-# entered, it will be relative to the location where doxygen was started. If
-# left blank the current directory will be used.
-
-OUTPUT_DIRECTORY = ./cpp
-
-# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
-# directories (in 2 levels) under the output directory of each output format and
-# will distribute the generated files over these directories. Enabling this
-# option can be useful when feeding doxygen a huge amount of source files, where
-# putting all generated files in the same directory would otherwise causes
-# performance problems for the file system.
-# The default value is: NO.
-
-CREATE_SUBDIRS = NO
-
-# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
-# characters to appear in the names of generated files. If set to NO, non-ASCII
-# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
-# U+3044.
-# The default value is: NO.
-
-ALLOW_UNICODE_NAMES = YES
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
-# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
-# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
-# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
-# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
-# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
-# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
-# Ukrainian and Vietnamese.
-# The default value is: English.
-
-OUTPUT_LANGUAGE = English
-
-# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
-# descriptions after the members that are listed in the file and class
-# documentation (similar to Javadoc). Set to NO to disable this.
-# The default value is: YES.
-
-BRIEF_MEMBER_DESC = YES
-
-# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
-# description of a member or function before the detailed description
-#
-# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
-# brief descriptions will be completely suppressed.
-# The default value is: YES.
-
-REPEAT_BRIEF = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator that is
-# used to form the text in various listings. Each string in this list, if found
-# as the leading text of the brief description, will be stripped from the text
-# and the result, after processing the whole list, is used as the annotated
-# text. Otherwise, the brief description is used as-is. If left blank, the
-# following values are used ($name is automatically replaced with the name of
-# the entity):The $name class, The $name widget, The $name file, is, provides,
-# specifies, contains, represents, a, an and the.
-
-ABBREVIATE_BRIEF =
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# doxygen will generate a detailed section even if there is only a brief
-# description.
-# The default value is: NO.
-
-ALWAYS_DETAILED_SEC = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-# The default value is: NO.
-
-INLINE_INHERITED_MEMB = NO
-
-# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
-# before files name in the file list and in the header files. If set to NO the
-# shortest path that makes the file name unique will be used
-# The default value is: YES.
-
-FULL_PATH_NAMES = YES
-
-# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
-# Stripping is only done if one of the specified strings matches the left-hand
-# part of the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the path to
-# strip.
-#
-# Note that you can specify absolute paths here, but also relative paths, which
-# will be relative from the directory where doxygen is started.
-# This tag requires that the tag FULL_PATH_NAMES is set to YES.
-
-STRIP_FROM_PATH =
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
-# path mentioned in the documentation of a class, which tells the reader which
-# header file to include in order to use a class. If left blank only the name of
-# the header file containing the class definition is used. Otherwise one should
-# specify the list of include paths that are normally passed to the compiler
-# using the -I flag.
-
-STRIP_FROM_INC_PATH =
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
-# less readable) file names. This can be useful is your file systems doesn't
-# support long names like on DOS, Mac, or CD-ROM.
-# The default value is: NO.
-
-SHORT_NAMES = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
-# first line (until the first dot) of a Javadoc-style comment as the brief
-# description. If set to NO, the Javadoc-style will behave just like regular Qt-
-# style comments (thus requiring an explicit @brief command for a brief
-# description.)
-# The default value is: NO.
-
-JAVADOC_AUTOBRIEF = NO
-
-# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
-# line (until the first dot) of a Qt-style comment as the brief description. If
-# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
-# requiring an explicit \brief command for a brief description.)
-# The default value is: NO.
-
-QT_AUTOBRIEF = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
-# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
-# a brief description. This used to be the default behavior. The new default is
-# to treat a multi-line C++ comment block as a detailed description. Set this
-# tag to YES if you prefer the old behavior instead.
-#
-# Note that setting this tag to YES also means that rational rose comments are
-# not recognized any more.
-# The default value is: NO.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
-# documentation from any documented member that it re-implements.
-# The default value is: YES.
-
-INHERIT_DOCS = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
-# page for each member. If set to NO, the documentation of a member will be part
-# of the file/class/namespace that contains it.
-# The default value is: NO.
-
-SEPARATE_MEMBER_PAGES = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
-# uses this value to replace tabs by spaces in code fragments.
-# Minimum value: 1, maximum value: 16, default value: 4.
-
-TAB_SIZE = 4
-
-# This tag can be used to specify a number of aliases that act as commands in
-# the documentation. An alias has the form:
-# name=value
-# For example adding
-# "sideeffect=@par Side Effects:\n"
-# will allow you to put the command \sideeffect (or @sideeffect) in the
-# documentation, which will result in a user-defined paragraph with heading
-# "Side Effects:". You can put \n's in the value part of an alias to insert
-# newlines.
-
-ALIASES =
-
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding "class=itcl::class"
-# will allow you to use the command class in the itcl::class meaning.
-
-TCL_SUBST =
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
-# only. Doxygen will then generate output that is more tailored for C. For
-# instance, some of the names that are used will be different. The list of all
-# members will be omitted, etc.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_FOR_C = NO
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
-# Python sources only. Doxygen will then generate output that is more tailored
-# for that language. For instance, namespaces will be presented as packages,
-# qualified scopes will look different, etc.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_JAVA = NO
-
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-# sources. Doxygen will then generate output that is tailored for Fortran.
-# The default value is: NO.
-
-OPTIMIZE_FOR_FORTRAN = NO
-
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-# sources. Doxygen will then generate output that is tailored for VHDL.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_VHDL = NO
-
-# Doxygen selects the parser to use depending on the extension of the files it
-# parses. With this tag you can assign which parser to use for a given
-# extension. Doxygen has a built-in mapping, but you can override or extend it
-# using this tag. The format is ext=language, where ext is a file extension, and
-# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
-# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
-# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
-# Fortran. In the later case the parser tries to guess whether the code is fixed
-# or free formatted code, this is the default for Fortran type files), VHDL. For
-# instance to make doxygen treat .inc files as Fortran files (default is PHP),
-# and .f files as C (default is Fortran), use: inc=Fortran f=C.
-#
-# Note: For files without extension you can use no_extension as a placeholder.
-#
-# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
-# the files are not read by doxygen.
-
-EXTENSION_MAPPING =
-
-# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
-# according to the Markdown format, which allows for more readable
-# documentation. See http://daringfireball.net/projects/markdown/ for details.
-# The output of markdown processing is further processed by doxygen, so you can
-# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
-# case of backward compatibilities issues.
-# The default value is: YES.
-
-MARKDOWN_SUPPORT = YES
-
-# When enabled doxygen tries to link words that correspond to documented
-# classes, or namespaces to their corresponding documentation. Such a link can
-# be prevented in individual cases by putting a % sign in front of the word or
-# globally by setting AUTOLINK_SUPPORT to NO.
-# The default value is: YES.
-
-AUTOLINK_SUPPORT = YES
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
-# to include (a tag file for) the STL sources as input, then you should set this
-# tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string);
-# versus func(std::string) {}). This also make the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-# The default value is: NO.
-
-BUILTIN_STL_SUPPORT = YES
-
-# If you use Microsoft's C++/CLI language, you should set this option to YES to
-# enable parsing support.
-# The default value is: NO.
-
-CPP_CLI_SUPPORT = NO
-
-# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
-# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
-# will parse them like normal C++ but will assume all classes use public instead
-# of private inheritance when no explicit protection keyword is present.
-# The default value is: NO.
-
-SIP_SUPPORT = YES
-
-# For Microsoft's IDL there are propget and propput attributes to indicate
-# getter and setter methods for a property. Setting this option to YES will make
-# doxygen to replace the get and set methods by a property in the documentation.
-# This will only work if the methods are indeed getting or setting a simple
-# type. If this is not the case, or you want to show the methods anyway, you
-# should set this option to NO.
-# The default value is: YES.
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-IDL_PROPERTY_SUPPORT = YES
-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
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-# The default value is: NO.
-
-DISTRIBUTE_GROUP_DOC = NO
-
-# Set the SUBGROUPING tag to YES to allow class member groups of the same type
-# (for instance a group of public functions) to be put as a subgroup of that
-# type (e.g. under the Public Functions section). Set it to NO to prevent
-# subgrouping. Alternatively, this can be done per class using the
-# \nosubgrouping command.
-# The default value is: YES.
-
-SUBGROUPING = YES
-
-# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
-# are shown inside the group in which they are included (e.g. using \ingroup)
-# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
-# and RTF).
-#
-# Note that this feature does not work in combination with
-# SEPARATE_MEMBER_PAGES.
-# The default value is: NO.
-
-INLINE_GROUPED_CLASSES = NO
-
-# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
-# with only public data fields or simple typedef fields will be shown inline in
-# the documentation of the scope in which they are defined (i.e. file,
-# namespace, or group documentation), provided this scope is documented. If set
-# to NO, structs, classes, and unions are shown on a separate page (for HTML and
-# Man pages) or section (for LaTeX and RTF).
-# The default value is: NO.
-
-INLINE_SIMPLE_STRUCTS = NO
-
-# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
-# enum is documented as struct, union, or enum with the name of the typedef. So
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
-# with name TypeT. When disabled the typedef will appear as a member of a file,
-# namespace, or class. And the struct will be named TypeS. This can typically be
-# useful for C code in case the coding convention dictates that all compound
-# types are typedef'ed and only the typedef is referenced, never the tag name.
-# The default value is: NO.
-
-TYPEDEF_HIDES_STRUCT = NO
-
-# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
-# cache is used to resolve symbols given their name and scope. Since this can be
-# an expensive process and often the same symbol appears multiple times in the
-# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
-# doxygen will become slower. If the cache is too large, memory is wasted. The
-# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
-# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
-# symbols. At the end of a run doxygen will report the cache usage and suggest
-# the optimal cache size from a speed point of view.
-# Minimum value: 0, maximum value: 9, default value: 0.
-
-LOOKUP_CACHE_SIZE = 0
-
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
-# documentation are documented, even if no documentation was available. Private
-# class members and static file members will be hidden unless the
-# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
-# Note: This will also disable the warnings about undocumented members that are
-# normally produced when WARNINGS is set to YES.
-# The default value is: NO.
-
-EXTRACT_ALL = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
-# be included in the documentation.
-# The default value is: NO.
-
-EXTRACT_PRIVATE = YES
-
-# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
-# scope will be included in the documentation.
-# The default value is: NO.
-
-EXTRACT_PACKAGE = YES
-
-# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
-# included in the documentation.
-# The default value is: NO.
-
-EXTRACT_STATIC = YES
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
-# locally in source files will be included in the documentation. If set to NO,
-# only classes defined in header files are included. Does not have any effect
-# for Java sources.
-# The default value is: YES.
-
-EXTRACT_LOCAL_CLASSES = YES
-
-# This flag is only useful for Objective-C code. If set to YES, local methods,
-# which are defined in the implementation section but not in the interface are
-# included in the documentation. If set to NO, only methods in the interface are
-# included.
-# The default value is: NO.
-
-EXTRACT_LOCAL_METHODS = YES
-
-# If this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base name of
-# the file that contains the anonymous namespace. By default anonymous namespace
-# are hidden.
-# The default value is: NO.
-
-EXTRACT_ANON_NSPACES = YES
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
-# undocumented members inside documented classes or files. If set to NO these
-# members will be included in the various overviews, but no documentation
-# section is generated. This option has no effect if EXTRACT_ALL is enabled.
-# The default value is: NO.
-
-HIDE_UNDOC_MEMBERS = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy. If set
-# to NO, these classes will be included in the various overviews. This option
-# has no effect if EXTRACT_ALL is enabled.
-# The default value is: NO.
-
-HIDE_UNDOC_CLASSES = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
-# (class|struct|union) declarations. If set to NO, these declarations will be
-# included in the documentation.
-# The default value is: NO.
-
-HIDE_FRIEND_COMPOUNDS = NO
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
-# documentation blocks found inside the body of a function. If set to NO, these
-# blocks will be appended to the function's detailed documentation block.
-# The default value is: NO.
-
-HIDE_IN_BODY_DOCS = NO
-
-# The INTERNAL_DOCS tag determines if documentation that is typed after a
-# \internal command is included. If the tag is set to NO then the documentation
-# will be excluded. Set it to YES to include the internal documentation.
-# The default value is: NO.
-
-INTERNAL_DOCS = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
-# names in lower-case letters. If set to YES, upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
-# The default value is: system dependent.
-
-CASE_SENSE_NAMES = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
-# their full class and namespace scopes in the documentation. If set to YES, the
-# scope will be hidden.
-# The default value is: NO.
-
-HIDE_SCOPE_NAMES = NO
-
-# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
-# append additional text to a page's title, such as Class Reference. If set to
-# YES the compound reference will be hidden.
-# The default value is: NO.
-
-HIDE_COMPOUND_REFERENCE= NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
-# the files that are included by a file in the documentation of that file.
-# The default value is: YES.
-
-SHOW_INCLUDE_FILES = YES
-
-# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
-# grouped member an include statement to the documentation, telling the reader
-# which file to include in order to use the member.
-# The default value is: NO.
-
-SHOW_GROUPED_MEMB_INC = NO
-
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
-# files with double quotes in the documentation rather than with sharp brackets.
-# The default value is: NO.
-
-FORCE_LOCAL_INCLUDES = NO
-
-# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
-# documentation for inline members.
-# The default value is: YES.
-
-INLINE_INFO = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
-# (detailed) documentation of file and class members alphabetically by member
-# name. If set to NO, the members will appear in declaration order.
-# The default value is: YES.
-
-SORT_MEMBER_DOCS = YES
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
-# descriptions of file, namespace and class members alphabetically by member
-# name. If set to NO, the members will appear in declaration order. Note that
-# this will also influence the order of the classes in the class list.
-# The default value is: NO.
-
-SORT_BRIEF_DOCS = YES
-
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
-# (brief and detailed) documentation of class members so that constructors and
-# destructors are listed first. If set to NO the constructors will appear in the
-# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
-# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
-# member documentation.
-# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
-# detailed member documentation.
-# The default value is: NO.
-
-SORT_MEMBERS_CTORS_1ST = NO
-
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
-# of group names into alphabetical order. If set to NO the group names will
-# appear in their defined order.
-# The default value is: NO.
-
-SORT_GROUP_NAMES = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
-# fully-qualified names, including namespaces. If set to NO, the class list will
-# be sorted only by class name, not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the alphabetical
-# list.
-# The default value is: NO.
-
-SORT_BY_SCOPE_NAME = NO
-
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
-# type resolution of all parameters of a function it will reject a match between
-# the prototype and the implementation of a member function even if there is
-# only one candidate or it is obvious which candidate to choose by doing a
-# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
-# accept a match between prototype and implementation in such cases.
-# The default value is: NO.
-
-STRICT_PROTO_MATCHING = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
-# list. This list is created by putting \todo commands in the documentation.
-# The default value is: YES.
-
-GENERATE_TODOLIST = NO
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
-# list. This list is created by putting \test commands in the documentation.
-# The default value is: YES.
-
-GENERATE_TESTLIST = NO
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
-# list. This list is created by putting \bug commands in the documentation.
-# The default value is: YES.
-
-GENERATE_BUGLIST = YES
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
-# the deprecated list. This list is created by putting \deprecated commands in
-# the documentation.
-# The default value is: YES.
-
-GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional documentation
-# sections, marked by \if <section_label> ... \endif and \cond <section_label>
-# ... \endcond blocks.
-
-ENABLED_SECTIONS =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
-# initial value of a variable or macro / define can have for it to appear in the
-# documentation. If the initializer consists of more lines than specified here
-# it will be hidden. Use a value of 0 to hide initializers completely. The
-# appearance of the value of individual variables and macros / defines can be
-# controlled using \showinitializer or \hideinitializer command in the
-# documentation regardless of this setting.
-# Minimum value: 0, maximum value: 10000, default value: 30.
-
-MAX_INITIALIZER_LINES = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
-# the bottom of the documentation of classes and structs. If set to YES, the
-# list will mention the files that were used to generate the documentation.
-# The default value is: YES.
-
-SHOW_USED_FILES = YES
-
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
-# will remove the Files entry from the Quick Index and from the Folder Tree View
-# (if specified).
-# The default value is: YES.
-
-SHOW_FILES = YES
-
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
-# page. This will remove the Namespaces entry from the Quick Index and from the
-# Folder Tree View (if specified).
-# The default value is: YES.
-
-SHOW_NAMESPACES = YES
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from
-# the version control system). Doxygen will invoke the program by executing (via
-# popen()) the command command input-file, where command is the value of the
-# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
-# by doxygen. Whatever the program writes to standard output is used as the file
-# version. For an example see the documentation.
-
-FILE_VERSION_FILTER =
-
-# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
-# by doxygen. The layout file controls the global structure of the generated
-# output files in an output format independent way. To create the layout file
-# that represents doxygen's defaults, run doxygen with the -l option. You can
-# optionally specify a file name after the option, if omitted DoxygenLayout.xml
-# will be used as the name of the layout file.
-#
-# Note that if you run doxygen from a directory containing a file called
-# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
-# tag is left empty.
-
-LAYOUT_FILE =
-
-# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
-# the reference definitions. This must be a list of .bib files. The .bib
-# extension is automatically appended if omitted. This requires the bibtex tool
-# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
-# For LaTeX the style of the bibliography can be controlled using
-# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
-# search path. See also \cite for info how to create references.
-
-CITE_BIB_FILES =
-
-#---------------------------------------------------------------------------
-# Configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated to
-# standard output by doxygen. If QUIET is set to YES this implies that the
-# messages are off.
-# The default value is: NO.
-
-QUIET = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
-# this implies that the warnings are on.
-#
-# Tip: Turn warnings on while writing the documentation.
-# The default value is: YES.
-
-WARNINGS = YES
-
-# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
-# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
-# will automatically be disabled.
-# The default value is: YES.
-
-WARN_IF_UNDOCUMENTED = YES
-
-# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some parameters
-# in a documented function, or documenting parameters that don't exist or using
-# markup commands wrongly.
-# The default value is: YES.
-
-WARN_IF_DOC_ERROR = YES
-
-# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
-# are documented, but have no documentation for their parameters or return
-# value. If set to NO, doxygen will only warn about wrong or incomplete
-# parameter documentation, but not about the absence of documentation.
-# The default value is: NO.
-
-WARN_NO_PARAMDOC = NO
-
-# The WARN_FORMAT tag determines the format of the warning messages that doxygen
-# can produce. The string should contain the $file, $line, and $text tags, which
-# will be replaced by the file and line number from which the warning originated
-# and the warning text. Optionally the format may contain $version, which will
-# be replaced by the version of the file (if it could be obtained via
-# FILE_VERSION_FILTER)
-# The default value is: $file:$line: $text.
-
-WARN_FORMAT = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning and error
-# messages should be written. If left blank the output is written to standard
-# error (stderr).
-
-WARN_LOGFILE = cpp/doxygen-logfile
-
-#---------------------------------------------------------------------------
-# Configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# The INPUT tag is used to specify the files and/or directories that contain
-# documented source files. You may enter file names like myfile.cpp or
-# directories like /usr/src/myproject. Separate the files or directories with
-# spaces.
-# Note: If this tag is empty the current directory is searched.
-
-INPUT = ../../basecode \
- ../../biophysics \
- ../../builtins \
- ../../device \
- ../../diffusion \
- ../../hsolve \
- ../../intfire \
- ../../kinetics \
- ../../ksolve \
- ../../mesh \
- ../../mpi \
- ../../msg \
- ../../randnum \
- ../../pymoose \
- ../../sbml \
- ../../scheduling \
- ../../shell \
- ../../signeur \
- ../../synapse \
- ../../utility
-
-
-# This tag can be used to specify the character encoding of the source files
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
-# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
-# documentation (see: http://www.gnu.org/software/libiconv) for the list of
-# possible encodings.
-# The default value is: UTF-8.
-
-INPUT_ENCODING = UTF-8
-
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
-# *.h) to filter out the source-files in the directories. If left blank the
-# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii,
-# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp,
-# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown,
-# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
-# *.qsf, *.as and *.js.
-
-FILE_PATTERNS = *.cpp \
- *.hpp \
- *.c \
- *.h \
- *.cc \
- *.hh \
- *.cxx \
- *.hxx
-
-
-# The RECURSIVE tag can be used to specify whether or not subdirectories should
-# be searched for input files as well.
-# The default value is: NO.
-
-RECURSIVE = YES
-
-# The EXCLUDE tag can be used to specify files and/or directories that should be
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-#
-# Note that relative paths are relative to the directory from which doxygen is
-# run.
-
-EXCLUDE =
-
-# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
-# directories that are symbolic links (a Unix file system feature) are excluded
-# from the input.
-# The default value is: NO.
-
-EXCLUDE_SYMLINKS = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories.
-#
-# Note that the wildcards are matched against the file with absolute path, so to
-# exclude all test directories for example use the pattern */test/*
-
-EXCLUDE_PATTERNS =
-
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
-# (namespaces, classes, functions, etc.) that should be excluded from the
-# output. The symbol name can be a fully qualified name, a word, or if the
-# wildcard * is used, a substring. Examples: ANamespace, AClass,
-# AClass::ANamespace, ANamespace::*Test
-#
-# Note that the wildcards are matched against the file with absolute path, so to
-# exclude all test directories use the pattern */test/*
-
-EXCLUDE_SYMBOLS =
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or directories
-# that contain example code fragments that are included (see the \include
-# command).
-
-EXAMPLE_PATH =
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
-# *.h) to filter out the source-files in the directories. If left blank all
-# files are included.
-
-EXAMPLE_PATTERNS =
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude commands
-# irrespective of the value of the RECURSIVE tag.
-# The default value is: NO.
-
-EXAMPLE_RECURSIVE = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or directories
-# that contain images that are to be included in the documentation (see the
-# \image command).
-
-IMAGE_PATH =
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command:
-#
-# <filter> <input-file>
-#
-# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
-# name of an input file. Doxygen will then use the output that the filter
-# program writes to standard output. If FILTER_PATTERNS is specified, this tag
-# will be ignored.
-#
-# Note that the filter must not add or remove lines; it is applied before the
-# code is scanned, but not when the output code is generated. If lines are added
-# or removed, the anchors will not be placed correctly.
-
-INPUT_FILTER =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form: pattern=filter
-# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
-# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
-# patterns match the file name, INPUT_FILTER is applied.
-
-FILTER_PATTERNS =
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will also be used to filter the input files that are used for
-# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
-# The default value is: NO.
-
-FILTER_SOURCE_FILES = NO
-
-# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
-# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
-# it is also possible to disable source filtering for a specific pattern using
-# *.ext= (so without naming a filter).
-# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
-
-FILTER_SOURCE_PATTERNS =
-
-# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
-# is part of the input, its contents will be placed on the main page
-# (index.html). This can be useful if you have a project on for instance GitHub
-# and want to reuse the introduction page also for the doxygen output.
-
-USE_MDFILE_AS_MAINPAGE =
-
-#---------------------------------------------------------------------------
-# Configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
-# generated. Documented entities will be cross-referenced with these sources.
-#
-# Note: To get rid of all source code in the generated output, make sure that
-# also VERBATIM_HEADERS is set to NO.
-# The default value is: NO.
-
-SOURCE_BROWSER = YES
-
-# Setting the INLINE_SOURCES tag to YES will include the body of functions,
-# classes and enums directly into the documentation.
-# The default value is: NO.
-
-INLINE_SOURCES = YES
-
-# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
-# special comment blocks from generated source code fragments. Normal C, C++ and
-# Fortran comments will always remain visible.
-# The default value is: YES.
-
-STRIP_CODE_COMMENTS = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
-# function all documented functions referencing it will be listed.
-# The default value is: NO.
-
-REFERENCED_BY_RELATION = YES
-
-# If the REFERENCES_RELATION tag is set to YES then for each documented function
-# all documented entities called/used by that function will be listed.
-# The default value is: NO.
-
-REFERENCES_RELATION = YES
-
-# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
-# to YES then the hyperlinks from functions in REFERENCES_RELATION and
-# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
-# link to the documentation.
-# The default value is: YES.
-
-REFERENCES_LINK_SOURCE = YES
-
-# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
-# source code will show a tooltip with additional information such as prototype,
-# brief description and links to the definition and documentation. Since this
-# will make the HTML file larger and loading of large files a bit slower, you
-# can opt to disable this feature.
-# The default value is: YES.
-# This tag requires that the tag SOURCE_BROWSER is set to YES.
-
-SOURCE_TOOLTIPS = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code will
-# point to the HTML generated by the htags(1) tool instead of doxygen built-in
-# source browser. The htags tool is part of GNU's global source tagging system
-# (see http://www.gnu.org/software/global/global.html). You will need version
-# 4.8.6 or higher.
-#
-# To use it do the following:
-# - Install the latest version of global
-# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
-# - Make sure the INPUT points to the root of the source tree
-# - Run doxygen as normal
-#
-# Doxygen will invoke htags (and that will in turn invoke gtags), so these
-# tools must be available from the command line (i.e. in the search path).
-#
-# The result: instead of the source browser generated by doxygen, the links to
-# source code will now point to the output of htags.
-# The default value is: NO.
-# This tag requires that the tag SOURCE_BROWSER is set to YES.
-
-USE_HTAGS = NO
-
-# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
-# verbatim copy of the header file for each class for which an include is
-# specified. Set to NO to disable this.
-# See also: Section \class.
-# The default value is: YES.
-
-VERBATIM_HEADERS = YES
-
-# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
-# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
-# cost of reduced performance. This can be particularly helpful with template
-# rich C++ code for which doxygen's built-in parser lacks the necessary type
-# information.
-# Note: The availability of this option depends on whether or not doxygen was
-# compiled with the --with-libclang option.
-# The default value is: NO.
-
-CLANG_ASSISTED_PARSING = YES
-
-# If clang assisted parsing is enabled you can provide the compiler with command
-# line options that you would normally use when invoking the compiler. Note that
-# the include paths will already be set by doxygen for the files and directories
-# specified with INPUT and INCLUDE_PATH.
-# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
-
-CLANG_OPTIONS = -std=c++11
-
-#---------------------------------------------------------------------------
-# Configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
-# compounds will be generated. Enable this if the project contains a lot of
-# classes, structs, unions or interfaces.
-# The default value is: YES.
-
-ALPHABETICAL_INDEX = YES
-
-# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
-# which the alphabetical index list will be split.
-# Minimum value: 1, maximum value: 20, default value: 5.
-# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
-
-COLS_IN_ALPHA_INDEX = 5
-
-# In case all classes in a project start with a common prefix, all classes will
-# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
-# can be used to specify a prefix (or a list of prefixes) that should be ignored
-# while generating the index headers.
-# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
-
-IGNORE_PREFIX =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
-# The default value is: YES.
-
-GENERATE_HTML = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: html.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_OUTPUT = html
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
-# generated HTML page (for example: .htm, .php, .asp).
-# The default value is: .html.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_FILE_EXTENSION = .html
-
-# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
-# each generated HTML page. If the tag is left blank doxygen will generate a
-# standard header.
-#
-# To get valid HTML the header file that includes any scripts and style sheets
-# that doxygen needs, which is dependent on the configuration options used (e.g.
-# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
-# default header using
-# doxygen -w html new_header.html new_footer.html new_stylesheet.css
-# YourConfigFile
-# and then modify the file new_header.html. See also section "Doxygen usage"
-# for information on how to generate the default header that doxygen normally
-# uses.
-# Note: The header is subject to change so you typically have to regenerate the
-# default header when upgrading to a newer version of doxygen. For a description
-# of the possible markers and block names see the documentation.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_HEADER =
-
-# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
-# generated HTML page. If the tag is left blank doxygen will generate a standard
-# footer. See HTML_HEADER for more information on how to generate a default
-# footer and what special commands can be used inside the footer. See also
-# section "Doxygen usage" for information on how to generate the default footer
-# that doxygen normally uses.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_FOOTER =
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
-# sheet that is used by each HTML page. It can be used to fine-tune the look of
-# the HTML output. If left blank doxygen will generate a default style sheet.
-# See also section "Doxygen usage" for information on how to generate the style
-# sheet that doxygen normally uses.
-# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
-# it is more robust and this tag (HTML_STYLESHEET) will in the future become
-# obsolete.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_STYLESHEET =
-
-# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
-# cascading style sheets that are included after the standard style sheets
-# created by doxygen. Using this option one can overrule certain style aspects.
-# This is preferred over using HTML_STYLESHEET since it does not replace the
-# standard style sheet and is therefore more robust against future updates.
-# Doxygen will copy the style sheet files to the output directory.
-# Note: The order of the extra style sheet files is of importance (e.g. the last
-# style sheet in the list overrules the setting of the previous ones in the
-# list). For an example see the documentation.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_EXTRA_STYLESHEET =
-
-# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
-# other source files which should be copied to the HTML output directory. Note
-# that these files will be copied to the base HTML output directory. Use the
-# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
-# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
-# files will be copied as-is; there are no commands or markers available.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_EXTRA_FILES =
-
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
-# will adjust the colors in the style sheet and background images according to
-# this color. Hue is specified as an angle on a colorwheel, see
-# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
-# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
-# purple, and 360 is red again.
-# Minimum value: 0, maximum value: 359, default value: 220.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_HUE = 220
-
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
-# in the HTML output. For a value of 0 the output will use grayscales only. A
-# value of 255 will produce the most vivid colors.
-# Minimum value: 0, maximum value: 255, default value: 100.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_SAT = 100
-
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
-# luminance component of the colors in the HTML output. Values below 100
-# gradually make the output lighter, whereas values above 100 make the output
-# darker. The value divided by 100 is the actual gamma applied, so 80 represents
-# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
-# change the gamma.
-# Minimum value: 40, maximum value: 240, default value: 80.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_GAMMA = 80
-
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting this
-# to NO can help when comparing the output of multiple runs.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_TIMESTAMP = YES
-
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
-# documentation will contain sections that can be hidden and shown after the
-# page has loaded.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_DYNAMIC_SECTIONS = YES
-
-# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
-# shown in the various tree structured indices initially; the user can expand
-# and collapse entries dynamically later on. Doxygen will expand the tree to
-# such a level that at most the specified number of entries are visible (unless
-# a fully collapsed tree already exceeds this amount). So setting the number of
-# entries 1 will produce a full collapsed tree by default. 0 is a special value
-# representing an infinite number of entries and will result in a full expanded
-# tree by default.
-# Minimum value: 0, maximum value: 9999, default value: 100.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_INDEX_NUM_ENTRIES = 100
-
-# If the GENERATE_DOCSET tag is set to YES, additional index files will be
-# generated that can be used as input for Apple's Xcode 3 integrated development
-# environment (see: http://developer.apple.com/tools/xcode/), introduced with
-# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
-# Makefile in the HTML output directory. Running make will produce the docset in
-# that directory and running make install will install the docset in
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
-# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
-# for more information.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_DOCSET = NO
-
-# This tag determines the name of the docset feed. A documentation feed provides
-# an umbrella under which multiple documentation sets from a single provider
-# (such as a company or product suite) can be grouped.
-# The default value is: Doxygen generated docs.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_FEEDNAME = "Doxygen generated docs"
-
-# This tag specifies a string that should uniquely identify the documentation
-# set bundle. This should be a reverse domain-name style string, e.g.
-# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
-# The default value is: org.doxygen.Project.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_BUNDLE_ID = org.doxygen.Project
-
-# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
-# the documentation publisher. This should be a reverse domain-name style
-# string, e.g. com.mycompany.MyDocSet.documentation.
-# The default value is: org.doxygen.Publisher.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_PUBLISHER_ID = org.doxygen.Publisher
-
-# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
-# The default value is: Publisher.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_PUBLISHER_NAME = Publisher
-
-# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
-# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
-# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
-# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
-# Windows.
-#
-# The HTML Help Workshop contains a compiler that can convert all HTML output
-# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
-# files are now used as the Windows 98 help format, and will replace the old
-# Windows help format (.hlp) on all Windows platforms in the future. Compressed
-# HTML files also contain an index, a table of contents, and you can search for
-# words in the documentation. The HTML workshop also contains a viewer for
-# compressed HTML files.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_HTMLHELP = NO
-
-# The CHM_FILE tag can be used to specify the file name of the resulting .chm
-# file. You can add a path in front of the file if the result should not be
-# written to the html output directory.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-CHM_FILE =
-
-# The HHC_LOCATION tag can be used to specify the location (absolute path
-# including file name) of the HTML help compiler (hhc.exe). If non-empty,
-# doxygen will try to run the HTML help compiler on the generated index.hhp.
-# The file has to be specified with full path.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-HHC_LOCATION =
-
-# The GENERATE_CHI flag controls if a separate .chi index file is generated
-# (YES) or that it should be included in the master .chm file (NO).
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-GENERATE_CHI = NO
-
-# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
-# and project file content.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-CHM_INDEX_ENCODING =
-
-# The BINARY_TOC flag controls whether a binary table of contents is generated
-# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
-# enables the Previous and Next buttons.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-BINARY_TOC = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members to
-# the table of contents of the HTML help documentation and to the tree view.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-TOC_EXPAND = NO
-
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
-# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
-# (.qch) of the generated HTML documentation.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_QHP = NO
-
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
-# the file name of the resulting .qch file. The path specified is relative to
-# the HTML output folder.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QCH_FILE =
-
-# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
-# Project output. For more information please see Qt Help Project / Namespace
-# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
-# The default value is: org.doxygen.Project.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_NAMESPACE = org.doxygen.Project
-
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
-# Help Project output. For more information please see Qt Help Project / Virtual
-# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
-# folders).
-# The default value is: doc.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_VIRTUAL_FOLDER = doc
-
-# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
-# filter to add. For more information please see Qt Help Project / Custom
-# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
-# filters).
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_CUST_FILTER_NAME =
-
-# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
-# custom filter to add. For more information please see Qt Help Project / Custom
-# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
-# filters).
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_CUST_FILTER_ATTRS =
-
-# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
-# project's filter section matches. Qt Help Project / Filter Attributes (see:
-# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_SECT_FILTER_ATTRS =
-
-# The QHG_LOCATION tag can be used to specify the location of Qt's
-# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
-# generated .qhp file.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHG_LOCATION =
-
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
-# generated, together with the HTML files, they form an Eclipse help plugin. To
-# install this plugin and make it available under the help contents menu in
-# Eclipse, the contents of the directory containing the HTML and XML files needs
-# to be copied into the plugins directory of eclipse. The name of the directory
-# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
-# After copying Eclipse needs to be restarted before the help appears.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_ECLIPSEHELP = NO
-
-# A unique identifier for the Eclipse help plugin. When installing the plugin
-# the directory name containing the HTML and XML files should also have this
-# name. Each documentation set should have its own identifier.
-# The default value is: org.doxygen.Project.
-# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
-
-ECLIPSE_DOC_ID = org.doxygen.Project
-
-# If you want full control over the layout of the generated HTML pages it might
-# be necessary to disable the index and replace it with your own. The
-# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
-# of each HTML page. A value of NO enables the index and the value YES disables
-# it. Since the tabs in the index contain the same information as the navigation
-# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-DISABLE_INDEX = NO
-
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information. If the tag
-# value is set to YES, a side panel will be generated containing a tree-like
-# index structure (just like the one that is generated for HTML Help). For this
-# to work a browser that supports JavaScript, DHTML, CSS and frames is required
-# (i.e. any modern browser). Windows users are probably better off using the
-# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
-# further fine-tune the look of the index. As an example, the default style
-# sheet generated by doxygen has an example that shows how to put an image at
-# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
-# the same information as the tab index, you could consider setting
-# DISABLE_INDEX to YES when enabling this option.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_TREEVIEW = YES
-
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
-# doxygen will group on one line in the generated HTML documentation.
-#
-# Note that a value of 0 will completely suppress the enum values from appearing
-# in the overview section.
-# Minimum value: 0, maximum value: 20, default value: 4.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-ENUM_VALUES_PER_LINE = 4
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
-# to set the initial width (in pixels) of the frame in which the tree is shown.
-# Minimum value: 0, maximum value: 1500, default value: 250.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-TREEVIEW_WIDTH = 250
-
-# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
-# external symbols imported via tag files in a separate window.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-EXT_LINKS_IN_WINDOW = NO
-
-# Use this tag to change the font size of LaTeX formulas included as images in
-# the HTML documentation. When you change the font size after a successful
-# doxygen run you need to manually remove any form_*.png images from the HTML
-# output directory to force them to be regenerated.
-# Minimum value: 8, maximum value: 50, default value: 10.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-FORMULA_FONTSIZE = 10
-
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are not
-# supported properly for IE 6.0, but are supported on all modern browsers.
-#
-# Note that when changing this option you need to delete any form_*.png files in
-# the HTML output directory before the changes have effect.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-FORMULA_TRANSPARENT = YES
-
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
-# http://www.mathjax.org) which uses client side Javascript for the rendering
-# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
-# installed or if you want to formulas look prettier in the HTML output. When
-# enabled you may also need to install MathJax separately and configure the path
-# to it using the MATHJAX_RELPATH option.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-USE_MATHJAX = YES
-
-# When MathJax is enabled you can set the default output format to be used for
-# the MathJax output. See the MathJax site (see:
-# http://docs.mathjax.org/en/latest/output.html) for more details.
-# Possible values are: HTML-CSS (which is slower, but has the best
-# compatibility), NativeMML (i.e. MathML) and SVG.
-# The default value is: HTML-CSS.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_FORMAT = HTML-CSS
-
-# When MathJax is enabled you need to specify the location relative to the HTML
-# output directory using the MATHJAX_RELPATH option. The destination directory
-# should contain the MathJax.js script. For instance, if the mathjax directory
-# is located at the same level as the HTML output directory, then
-# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
-# Content Delivery Network so you can quickly see the result without installing
-# MathJax. However, it is strongly recommended to install a local copy of
-# MathJax from http://www.mathjax.org before deployment.
-# The default value is: http://cdn.mathjax.org/mathjax/latest.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
-
-# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
-# extension names that should be enabled during MathJax rendering. For example
-# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_EXTENSIONS =
-
-# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
-# of code that will be used on startup of the MathJax code. See the MathJax site
-# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
-# example see the documentation.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_CODEFILE =
-
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
-# the HTML output. The underlying search engine uses javascript and DHTML and
-# should work on any modern browser. Note that when using HTML help
-# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
-# there is already a search function so this one should typically be disabled.
-# For large projects the javascript based search engine can be slow, then
-# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
-# search using the keyboard; to jump to the search box use <access key> + S
-# (what the <access key> is depends on the OS and browser, but it is typically
-# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
-# key> to jump into the search results window, the results can be navigated
-# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
-# the search. The filter options can be selected when the cursor is inside the
-# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
-# to select a filter and <Enter> or <escape> to activate or cancel the filter
-# option.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-SEARCHENGINE = YES
-
-# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a web server instead of a web client using Javascript. There
-# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
-# setting. When disabled, doxygen will generate a PHP script for searching and
-# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
-# and searching needs to be provided by external tools. See the section
-# "External Indexing and Searching" for details.
-# The default value is: NO.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-SERVER_BASED_SEARCH = NO
-
-# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
-# script for searching. Instead the search results are written to an XML file
-# which needs to be processed by an external indexer. Doxygen will invoke an
-# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
-# search results.
-#
-# Doxygen ships with an example indexer (doxyindexer) and search engine
-# (doxysearch.cgi) which are based on the open source search engine library
-# Xapian (see: http://xapian.org/).
-#
-# See the section "External Indexing and Searching" for details.
-# The default value is: NO.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-EXTERNAL_SEARCH = NO
-
-# The SEARCHENGINE_URL should point to a search engine hosted by a web server
-# which will return the search results when EXTERNAL_SEARCH is enabled.
-#
-# Doxygen ships with an example indexer (doxyindexer) and search engine
-# (doxysearch.cgi) which are based on the open source search engine library
-# Xapian (see: http://xapian.org/). See the section "External Indexing and
-# Searching" for details.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-SEARCHENGINE_URL =
-
-# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
-# search data is written to a file for indexing by an external tool. With the
-# SEARCHDATA_FILE tag the name of this file can be specified.
-# The default file is: searchdata.xml.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-SEARCHDATA_FILE = searchdata.xml
-
-# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
-# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
-# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
-# projects and redirect the results back to the right project.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-EXTERNAL_SEARCH_ID =
-
-# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
-# projects other than the one defined by this configuration file, but that are
-# all added to the same external search index. Each project needs to have a
-# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
-# to a relative location where the documentation can be found. The format is:
-# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-EXTRA_SEARCH_MAPPINGS =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
-# The default value is: YES.
-
-GENERATE_LATEX = NO
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: latex.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_OUTPUT = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked.
-#
-# Note that when enabling USE_PDFLATEX this option is only used for generating
-# bitmaps for formulas in the HTML output, but not in the Makefile that is
-# written to the output directory.
-# The default file is: latex.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_CMD_NAME = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
-# index for LaTeX.
-# The default file is: makeindex.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-MAKEINDEX_CMD_NAME = makeindex
-
-# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
-# documents. This may be useful for small projects and may help to save some
-# trees in general.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-COMPACT_LATEX = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used by the
-# printer.
-# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
-# 14 inches) and executive (7.25 x 10.5 inches).
-# The default value is: a4.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-PAPER_TYPE = a4
-
-# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
-# that should be included in the LaTeX output. To get the times font for
-# instance you can specify
-# EXTRA_PACKAGES=times
-# If left blank no extra packages will be included.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-EXTRA_PACKAGES =
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
-# generated LaTeX document. The header should contain everything until the first
-# chapter. If it is left blank doxygen will generate a standard header. See
-# section "Doxygen usage" for information on how to let doxygen write the
-# default header to a separate file.
-#
-# Note: Only use a user-defined header if you know what you are doing! The
-# following commands have a special meaning inside the header: $title,
-# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
-# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
-# string, for the replacement values of the other commands the user is referred
-# to HTML_HEADER.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_HEADER =
-
-# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
-# generated LaTeX document. The footer should contain everything after the last
-# chapter. If it is left blank doxygen will generate a standard footer. See
-# LATEX_HEADER for more information on how to generate a default footer and what
-# special commands can be used inside the footer.
-#
-# Note: Only use a user-defined footer if you know what you are doing!
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_FOOTER =
-
-# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
-# LaTeX style sheets that are included after the standard style sheets created
-# by doxygen. Using this option one can overrule certain style aspects. Doxygen
-# will copy the style sheet files to the output directory.
-# Note: The order of the extra style sheet files is of importance (e.g. the last
-# style sheet in the list overrules the setting of the previous ones in the
-# list).
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_EXTRA_STYLESHEET =
-
-# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
-# other source files which should be copied to the LATEX_OUTPUT output
-# directory. Note that the files will be copied as-is; there are no commands or
-# markers available.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_EXTRA_FILES =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
-# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
-# contain links (just like the HTML output) instead of page references. This
-# makes the output suitable for online browsing using a PDF viewer.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-PDF_HYPERLINKS = YES
-
-# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
-# the PDF file directly from the LaTeX files. Set this option to YES, to get a
-# higher quality PDF documentation.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-USE_PDFLATEX = YES
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
-# command to the generated LaTeX files. This will instruct LaTeX to keep running
-# if errors occur, instead of asking the user for help. This option is also used
-# when generating formulas in HTML.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_BATCHMODE = NO
-
-# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
-# index chapters (such as File Index, Compound Index, etc.) in the output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_HIDE_INDICES = NO
-
-# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
-# code with syntax highlighting in the LaTeX output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_SOURCE_CODE = NO
-
-# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
-# bibliography, e.g. plainnat, or ieeetr. See
-# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
-# The default value is: plain.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_BIB_STYLE = plain
-
-#---------------------------------------------------------------------------
-# Configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
-# RTF output is optimized for Word 97 and may not look too pretty with other RTF
-# readers/editors.
-# The default value is: NO.
-
-GENERATE_RTF = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: rtf.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_OUTPUT = rtf
-
-# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
-# documents. This may be useful for small projects and may help to save some
-# trees in general.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-COMPACT_RTF = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
-# contain hyperlink fields. The RTF file will contain links (just like the HTML
-# output) instead of page references. This makes the output suitable for online
-# browsing using Word or some other Word compatible readers that support those
-# fields.
-#
-# Note: WordPad (write) and others do not support links.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_HYPERLINKS = NO
-
-# Load stylesheet definitions from file. Syntax is similar to doxygen's config
-# file, i.e. a series of assignments. You only have to provide replacements,
-# missing definitions are set to their default value.
-#
-# See also section "Doxygen usage" for information on how to generate the
-# default style sheet that doxygen normally uses.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_STYLESHEET_FILE =
-
-# Set optional variables used in the generation of an RTF document. Syntax is
-# similar to doxygen's config file. A template extensions file can be generated
-# using doxygen -e rtf extensionFile.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_EXTENSIONS_FILE =
-
-# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
-# with syntax highlighting in the RTF output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_SOURCE_CODE = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
-# classes and files.
-# The default value is: NO.
-
-GENERATE_MAN = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it. A directory man3 will be created inside the directory specified by
-# MAN_OUTPUT.
-# The default directory is: man.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-MAN_OUTPUT = man
-
-# The MAN_EXTENSION tag determines the extension that is added to the generated
-# man pages. In case the manual section does not start with a number, the number
-# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
-# optional.
-# The default value is: .3.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-MAN_EXTENSION = .3
-
-# The MAN_SUBDIR tag determines the name of the directory created within
-# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
-# MAN_EXTENSION with the initial . removed.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-MAN_SUBDIR =
-
-# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
-# will generate one additional man file for each entity documented in the real
-# man page(s). These additional files only source the real man page, but without
-# them the man command would be unable to find the correct page.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-MAN_LINKS = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the XML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
-# captures the structure of the code including all documentation.
-# The default value is: NO.
-
-GENERATE_XML = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: xml.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_OUTPUT = xml
-
-# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
-# listings (including syntax highlighting and cross-referencing information) to
-# the XML output. Note that enabling this will significantly increase the size
-# of the XML output.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_PROGRAMLISTING = YES
-
-#---------------------------------------------------------------------------
-# Configuration options related to the DOCBOOK output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
-# that can be used to generate PDF.
-# The default value is: NO.
-
-GENERATE_DOCBOOK = NO
-
-# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
-# front of it.
-# The default directory is: docbook.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_OUTPUT = docbook
-
-# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
-# program listings (including syntax highlighting and cross-referencing
-# information) to the DOCBOOK output. Note that enabling this will significantly
-# increase the size of the DOCBOOK output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_PROGRAMLISTING = NO
-
-#---------------------------------------------------------------------------
-# Configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
-# AutoGen Definitions (see http://autogen.sf.net) file that captures the
-# structure of the code including all documentation. Note that this feature is
-# still experimental and incomplete at the moment.
-# The default value is: NO.
-
-GENERATE_AUTOGEN_DEF = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
-# file that captures the structure of the code including all documentation.
-#
-# Note that this feature is still experimental and incomplete at the moment.
-# The default value is: NO.
-
-GENERATE_PERLMOD = NO
-
-# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
-# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
-# output from the Perl module output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-
-PERLMOD_LATEX = NO
-
-# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
-# formatted so it can be parsed by a human reader. This is useful if you want to
-# understand what is going on. On the other hand, if this tag is set to NO, the
-# size of the Perl module output will be much smaller and Perl will parse it
-# just the same.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-
-PERLMOD_PRETTY = YES
-
-# The names of the make variables in the generated doxyrules.make file are
-# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
-# so different doxyrules.make files included by the same Makefile don't
-# overwrite each other's variables.
-# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-
-PERLMOD_MAKEVAR_PREFIX =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
-#---------------------------------------------------------------------------
-
-# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
-# C-preprocessor directives found in the sources and include files.
-# The default value is: YES.
-
-ENABLE_PREPROCESSING = YES
-
-# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
-# in the source code. If set to NO, only conditional compilation will be
-# performed. Macro expansion can be done in a controlled way by setting
-# EXPAND_ONLY_PREDEF to YES.
-# The default value is: NO.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-MACRO_EXPANSION = NO
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
-# the macro expansion is limited to the macros specified with the PREDEFINED and
-# EXPAND_AS_DEFINED tags.
-# The default value is: NO.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-EXPAND_ONLY_PREDEF = NO
-
-# If the SEARCH_INCLUDES tag is set to YES, the include files in the
-# INCLUDE_PATH will be searched if a #include is found.
-# The default value is: YES.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-SEARCH_INCLUDES = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by the
-# preprocessor.
-# This tag requires that the tag SEARCH_INCLUDES is set to YES.
-
-INCLUDE_PATH =
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will be
-# used.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-INCLUDE_FILE_PATTERNS =
-
-# The PREDEFINED tag can be used to specify one or more macro names that are
-# defined before the preprocessor is started (similar to the -D option of e.g.
-# gcc). The argument of the tag is a list of macros of the form: name or
-# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
-# is assumed. To prevent a macro definition from being undefined via #undef or
-# recursively expanded use the := operator instead of the = operator.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-PREDEFINED =
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
-# tag can be used to specify a list of macro names that should be expanded. The
-# macro definition that is found in the sources will be used. Use the PREDEFINED
-# tag if you want to use a different macro definition that overrules the
-# definition found in the source code.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-EXPAND_AS_DEFINED =
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
-# remove all references to function-like macros that are alone on a line, have
-# an all uppercase name, and do not end with a semicolon. Such function macros
-# are typically used for boiler-plate code, and will confuse the parser if not
-# removed.
-# The default value is: YES.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-SKIP_FUNCTION_MACROS = YES
-
-#---------------------------------------------------------------------------
-# Configuration options related to external references
-#---------------------------------------------------------------------------
-
-# The TAGFILES tag can be used to specify one or more tag files. For each tag
-# file the location of the external documentation should be added. The format of
-# a tag file without this location is as follows:
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where loc1 and loc2 can be relative or absolute paths or URLs. See the
-# section "Linking to external documentation" for more information about the use
-# of tag files.
-# Note: Each tag file must have a unique name (where the name does NOT include
-# the path). If a tag file is not located in the directory in which doxygen is
-# run, you must also specify the path to the tagfile here.
-
-TAGFILES =
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
-# tag file that is based on the input files it reads. See section "Linking to
-# external documentation" for more information about the usage of tag files.
-
-GENERATE_TAGFILE =
-
-# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
-# the class index. If set to NO, only the inherited external classes will be
-# listed.
-# The default value is: NO.
-
-ALLEXTERNALS = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will be
-# listed.
-# The default value is: YES.
-
-EXTERNAL_GROUPS = YES
-
-# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
-# the related pages index. If set to NO, only the current project's pages will
-# be listed.
-# The default value is: YES.
-
-EXTERNAL_PAGES = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of 'which perl').
-# The default file (with absolute path) is: /usr/bin/perl.
-
-PERL_PATH = /usr/bin/perl
-
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
-# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
-# NO turns the diagrams off. Note that this option also works with HAVE_DOT
-# disabled, but it is recommended to install and use dot, since it yields more
-# powerful graphs.
-# The default value is: YES.
-
-CLASS_DIAGRAMS = YES
-
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see:
-# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
-# the mscgen tool resides. If left empty the tool is assumed to be found in the
-# default search path.
-
-MSCGEN_PATH =
-
-# You can include diagrams made with dia in doxygen documentation. Doxygen will
-# then run dia to produce the diagram and insert it in the documentation. The
-# DIA_PATH tag allows you to specify the directory where the dia binary resides.
-# If left empty dia is assumed to be found in the default search path.
-
-DIA_PATH =
-
-# If set to YES the inheritance and collaboration graphs will hide inheritance
-# and usage relations if the target is undocumented or is not a class.
-# The default value is: YES.
-
-HIDE_UNDOC_RELATIONS = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz (see:
-# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
-# Bell Labs. The other options in this section have no effect if this option is
-# set to NO
-# The default value is: YES.
-
-HAVE_DOT = YES
-
-# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
-# to run in parallel. When set to 0 doxygen will base this on the number of
-# processors available in the system. You can set it explicitly to a value
-# larger than 0 to get control over the balance between CPU load and processing
-# speed.
-# Minimum value: 0, maximum value: 32, default value: 0.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_NUM_THREADS = 0
-
-# When you want a differently looking font in the dot files that doxygen
-# generates you can specify the font name using DOT_FONTNAME. You need to make
-# sure dot is able to find the font, which can be done by putting it in a
-# standard location or by setting the DOTFONTPATH environment variable or by
-# setting DOT_FONTPATH to the directory containing the font.
-# The default value is: Helvetica.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_FONTNAME = Ubuntu Mono
-
-# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
-# dot graphs.
-# Minimum value: 4, maximum value: 24, default value: 10.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_FONTSIZE = 10
-
-# By default doxygen will tell dot to use the default font as specified with
-# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
-# the path where dot can find it using this tag.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_FONTPATH =
-
-# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
-# each documented class showing the direct and indirect inheritance relations.
-# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-CLASS_GRAPH = YES
-
-# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
-# graph for each documented class showing the direct and indirect implementation
-# dependencies (inheritance, containment, and class references variables) of the
-# class with other documented classes.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-COLLABORATION_GRAPH = YES
-
-# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
-# groups, showing the direct groups dependencies.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-GROUP_GRAPHS = YES
-
-# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
-# Language.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-UML_LOOK = YES
-
-# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
-# class node. If there are many fields or methods and many nodes the graph may
-# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
-# number of items for each type to make the size more manageable. Set this to 0
-# for no limit. Note that the threshold may be exceeded by 50% before the limit
-# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
-# but if the number exceeds 15, the total amount of fields shown is limited to
-# 10.
-# Minimum value: 0, maximum value: 100, default value: 10.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-UML_LIMIT_NUM_FIELDS = 10
-
-# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
-# collaboration graphs will show the relations between templates and their
-# instances.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-TEMPLATE_RELATIONS = YES
-
-# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
-# YES then doxygen will generate a graph for each documented file showing the
-# direct and indirect include dependencies of the file with other documented
-# files.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-INCLUDE_GRAPH = YES
-
-# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
-# set to YES then doxygen will generate a graph for each documented file showing
-# the direct and indirect include dependencies of the file with other documented
-# files.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-INCLUDED_BY_GRAPH = YES
-
-# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
-# dependency graph for every global function or class method.
-#
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-CALL_GRAPH = YES
-
-# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
-# dependency graph for every global function or class method.
-#
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable caller graphs for selected
-# functions only using the \callergraph command.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-CALLER_GRAPH = YES
-
-# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
-# hierarchy of all classes instead of a textual one.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-GRAPHICAL_HIERARCHY = YES
-
-# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
-# dependencies a directory has on other directories in a graphical way. The
-# dependency relations are determined by the #include relations between the
-# files in the directories.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DIRECTORY_GRAPH = YES
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot.
-# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
-# to make the SVG files visible in IE 9+ (other browsers do not have this
-# requirement).
-# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd,
-# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo,
-# gif:cairo:gd, gif:gd, gif:gd:gd and svg.
-# The default value is: png.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_IMAGE_FORMAT = svg
-
-# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
-# enable generation of interactive SVG images that allow zooming and panning.
-#
-# Note that this requires a modern browser other than Internet Explorer. Tested
-# and working are Firefox, Chrome, Safari, and Opera.
-# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
-# the SVG files visible. Older versions of IE do not have SVG support.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-INTERACTIVE_SVG = YES
-
-# The DOT_PATH tag can be used to specify the path where the dot tool can be
-# found. If left blank, it is assumed the dot tool can be found in the path.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_PATH =
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the \dotfile
-# command).
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOTFILE_DIRS =
-
-# The MSCFILE_DIRS tag can be used to specify one or more directories that
-# contain msc files that are included in the documentation (see the \mscfile
-# command).
-
-MSCFILE_DIRS =
-
-# The DIAFILE_DIRS tag can be used to specify one or more directories that
-# contain dia files that are included in the documentation (see the \diafile
-# command).
-
-DIAFILE_DIRS =
-
-# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
-# path where java can find the plantuml.jar file. If left blank, it is assumed
-# PlantUML is not used or called during a preprocessing step. Doxygen will
-# generate a warning when it encounters a \startuml command in this case and
-# will not generate output for the diagram.
-
-PLANTUML_JAR_PATH =
-
-# When using plantuml, the specified paths are searched for files specified by
-# the !include statement in a plantuml block.
-
-PLANTUML_INCLUDE_PATH =
-
-# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
-# that will be shown in the graph. If the number of nodes in a graph becomes
-# larger than this value, doxygen will truncate the graph, which is visualized
-# by representing a node as a red box. Note that doxygen if the number of direct
-# children of the root node in a graph is already larger than
-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
-# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
-# Minimum value: 0, maximum value: 10000, default value: 50.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_GRAPH_MAX_NODES = 50
-
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
-# generated by dot. A depth value of 3 means that only nodes reachable from the
-# root by following a path via at most 3 edges will be shown. Nodes that lay
-# further from the root node will be omitted. Note that setting this option to 1
-# or 2 may greatly reduce the computation time needed for large code bases. Also
-# note that the size of a graph can be further restricted by
-# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
-# Minimum value: 0, maximum value: 1000, default value: 0.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-MAX_DOT_GRAPH_DEPTH = 0
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not seem
-# to support this out of the box.
-#
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_TRANSPARENT = NO
-
-# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
-# files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10) support
-# this, this feature is disabled by default.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_MULTI_TARGETS = YES
-
-# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
-# explaining the meaning of the various boxes and arrows in the dot generated
-# graphs.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-GENERATE_LEGEND = YES
-
-# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
-# files that are used to generate the various graphs.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_CLEANUP = YES
diff --git a/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile b/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile
deleted file mode 100644
index 73ede6e3c46e3c4d8770aea5f5e67aa77fd055bf..0000000000000000000000000000000000000000
--- a/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile
+++ /dev/null
@@ -1,1237 +0,0 @@
-# Doxyfile 1.4.6
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
-#
-# All text after a hash (#) is considered a comment and will be ignored
-# The format is:
-# TAG = value [value, ...]
-# For lists items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
-# by quotes) that should identify the project.
-
-PROJECT_NAME = MOOSE
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
-
-PROJECT_NUMBER =
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
-
-OUTPUT_DIRECTORY = ./Docs/developer
-
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-# 4096 sub-directories (in 2 levels) under the output directory of each output
-# format and will distribute the generated files over these directories.
-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
-
-CREATE_SUBDIRS = NO
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish,
-# Dutch, Finnish, French, German, Greek, Hungarian, Italian, Japanese,
-# Japanese-en (Japanese with English messages), Korean, Korean-en, Norwegian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish,
-# Swedish, and Ukrainian.
-
-OUTPUT_LANGUAGE = English
-
-# This tag can be used to specify the encoding used in the generated output.
-# The encoding is not always determined by the language that is chosen,
-# but also whether or not the output is meant for Windows or non-Windows users.
-# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES
-# forces the Windows encoding (this is the default for the Windows binary),
-# whereas setting the tag to NO uses a Unix-style encoding (the default for
-# all platforms other than Windows).
-
-USE_WINDOWS_ENCODING = NO
-
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
-
-BRIEF_MEMBER_DESC = YES
-
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
-# brief descriptions will be completely suppressed.
-
-REPEAT_BRIEF = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator
-# that is used to form the text in various listings. Each string
-# in this list, if found as the leading text of the brief description, will be
-# stripped from the text and the result after processing the whole list, is
-# used as the annotated text. Otherwise, the brief description is used as-is.
-# If left blank, the following values are used ("$name" is automatically
-# replaced with the name of the entity): "The $name class" "The $name widget"
-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
-
-ABBREVIATE_BRIEF =
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
-# description.
-
-ALWAYS_DETAILED_SEC = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-
-INLINE_INHERITED_MEMB = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-# path before files name in the file list and in the header files. If set
-# to NO the shortest path that makes the file name unique will be used.
-
-FULL_PATH_NAMES = YES
-
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
-
-STRIP_FROM_PATH =
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-# the path mentioned in the documentation of a class, which tells
-# the reader which header file to include in order to use a class.
-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
-
-STRIP_FROM_INC_PATH =
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful is your file systems
-# doesn't support long names like on DOS, Mac, or CD-ROM.
-
-SHORT_NAMES = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like the Qt-style comments (thus requiring an
-# explicit @brief command for a brief description.
-
-JAVADOC_AUTOBRIEF = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
-# description. Set this tag to YES if you prefer the old behaviour instead.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the DETAILS_AT_TOP tag is set to YES then Doxygen
-# will output the detailed description near the top, like JavaDoc.
-# If set to NO, the detailed description appears after the member
-# documentation.
-
-DETAILS_AT_TOP = NO
-
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
-
-INHERIT_DOCS = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
-
-SEPARATE_MEMBER_PAGES = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
-
-TAB_SIZE = 4
-
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
-
-ALIASES =
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
-
-OPTIMIZE_OUTPUT_FOR_C = NO
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for Java.
-# For instance, namespaces will be presented as packages, qualified scopes
-# will look different, etc.
-
-OPTIMIZE_OUTPUT_JAVA = NO
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to
-# include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also make the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-
-BUILTIN_STL_SUPPORT = YES
-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
-# all members of a group must be documented explicitly.
-
-DISTRIBUTE_GROUP_DOC = NO
-
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
-
-SUBGROUPING = YES
-
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
-EXTRACT_ALL = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
-
-EXTRACT_PRIVATE = NO
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
-
-EXTRACT_STATIC = NO
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
-EXTRACT_LOCAL_METHODS = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_MEMBERS = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS = NO
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
-
-HIDE_IN_BODY_DOCS = NO
-
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
-
-INTERNAL_DOCS = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
-
-CASE_SENSE_NAMES = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
-
-HIDE_SCOPE_NAMES = NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
-
-SHOW_INCLUDE_FILES = YES
-
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
-
-INLINE_INFO = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
-
-SORT_MEMBER_DOCS = YES
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
-
-SORT_BRIEF_DOCS = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
-
-SORT_BY_SCOPE_NAME = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
-
-GENERATE_TODOLIST = YES
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
-
-GENERATE_TESTLIST = YES
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
-
-GENERATE_BUGLIST = YES
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
-
-GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
-
-ENABLED_SECTIONS =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or define consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and defines in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
-
-MAX_INITIALIZER_LINES = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
-# list will mention the files that were used to generate the documentation.
-
-SHOW_USED_FILES = YES
-
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES = NO
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from the
-# version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
-
-FILE_VERSION_FILTER =
-
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
-
-QUIET = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
-
-WARNINGS = YES
-
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
-
-WARN_IF_UNDOCUMENTED = YES
-
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
-
-WARN_IF_DOC_ERROR = YES
-
-# This WARN_NO_PARAMDOC option can be abled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
-
-WARN_NO_PARAMDOC = NO
-
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
-
-WARN_FORMAT = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
-
-WARN_LOGFILE =
-
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
-
-INPUT = ./Docs ./basecode ./biophysics ./builtins ./device ./geom ./hsolve ./kinetics ./ksolve ./manager ./mesh ./msg ./randnum ./sbml ./scheduling ./shell ./signeur ./smol ./testReduce ./threadTests ./utility
-
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
-
-FILE_PATTERNS =
-
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
-
-RECURSIVE = YES
-
-# The EXCLUDE tag can be used to specify files and/or directories that should
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-
-EXCLUDE =
-
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
-# directories that are symbolic links (a Unix filesystem feature) are excluded
-# from the input.
-
-EXCLUDE_SYMLINKS = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
-
-EXCLUDE_PATTERNS = *.py */.svn/*
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
-
-EXAMPLE_PATH =
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
-
-EXAMPLE_PATTERNS =
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
-
-EXAMPLE_RECURSIVE = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
-
-IMAGE_PATH = ./Docs/images
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output. If FILTER_PATTERNS is specified, this tag will be
-# ignored.
-
-INPUT_FILTER =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
-# is applied to all files.
-
-FILTER_PATTERNS =
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
-
-FILTER_SOURCE_FILES = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
-
-SOURCE_BROWSER = NO
-
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
-
-INLINE_SOURCES = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C and C++ comments will always remain visible.
-
-STRIP_CODE_COMMENTS = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES (the default)
-# then for each documented function all documented
-# functions referencing it will be listed.
-
-REFERENCED_BY_RELATION = YES
-
-# If the REFERENCES_RELATION tag is set to YES (the default)
-# then for each documented function all documented entities
-# called/used by that function will be listed.
-
-REFERENCES_RELATION = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
-
-USE_HTAGS = NO
-
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
-
-VERBATIM_HEADERS = YES
-
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
-
-ALPHABETICAL_INDEX = NO
-
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
-
-COLS_IN_ALPHA_INDEX = 5
-
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
-
-IGNORE_PREFIX =
-
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
-
-GENERATE_HTML = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
-
-HTML_OUTPUT = html
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
-
-HTML_FILE_EXTENSION = .html
-
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header.
-
-HTML_HEADER =
-
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
-
-HTML_FOOTER =
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# stylesheet in the HTML output directory as well, or it will be erased!
-
-HTML_STYLESHEET =
-
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS = YES
-
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compressed HTML help file (.chm)
-# of the generated HTML documentation.
-
-GENERATE_HTMLHELP = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
-# written to the html output directory.
-
-CHM_FILE =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
-
-HHC_LOCATION =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
-
-GENERATE_CHI = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
-
-BINARY_TOC = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
-
-TOC_EXPAND = NO
-
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
-# top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it.
-
-DISABLE_INDEX = NO
-
-# This tag can be used to set the number of enum values (range [1..20])
-# that doxygen will group on one line in the generated HTML documentation.
-
-ENUM_VALUES_PER_LINE = 4
-
-# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
-# generated containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
-# probably better off using the HTML help feature.
-
-GENERATE_TREEVIEW = NO
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
-
-TREEVIEW_WIDTH = 250
-
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
-
-GENERATE_LATEX = NO
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
-
-LATEX_OUTPUT = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-
-LATEX_CMD_NAME = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
-
-MAKEINDEX_CMD_NAME = makeindex
-
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_LATEX = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, a4wide, letter, legal and
-# executive. If left blank a4wide will be used.
-
-PAPER_TYPE = a4wide
-
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
-
-EXTRA_PACKAGES =
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
-
-LATEX_HEADER =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
-
-PDF_HYPERLINKS = NO
-
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
-# higher quality PDF documentation.
-
-USE_PDFLATEX = NO
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
-
-LATEX_BATCHMODE = NO
-
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
-
-LATEX_HIDE_INDICES = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
-
-GENERATE_RTF = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
-
-RTF_OUTPUT = rtf
-
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_RTF = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
-
-RTF_HYPERLINKS = NO
-
-# Load stylesheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
-
-RTF_STYLESHEET_FILE =
-
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
-
-RTF_EXTENSIONS_FILE =
-
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
-
-GENERATE_MAN = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
-
-MAN_OUTPUT = man
-
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
-
-MAN_EXTENSION = .3
-
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
-
-MAN_LINKS = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
-
-GENERATE_XML = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
-
-XML_OUTPUT = xml
-
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_SCHEMA =
-
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_DTD =
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
-
-XML_PROGRAMLISTING = YES
-
-#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
-
-GENERATE_AUTOGEN_DEF = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
-
-GENERATE_PERLMOD = NO
-
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
-
-PERLMOD_LATEX = NO
-
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader. This is useful
-# if you want to understand what is going on. On the other hand, if this
-# tag is set to NO the size of the Perl module output will be much smaller
-# and Perl will parse it just the same.
-
-PERLMOD_PRETTY = YES
-
-# The names of the make variables in the generated doxyrules.make file
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-# This is useful so different doxyrules.make files included by the same
-# Makefile don't overwrite each other's variables.
-
-PERLMOD_MAKEVAR_PREFIX =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
-#---------------------------------------------------------------------------
-
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-# evaluate all C-preprocessor directives found in the sources and include
-# files.
-
-ENABLE_PREPROCESSING = YES
-
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-# names in the source code. If set to NO (the default) only conditional
-# compilation will be performed. Macro expansion can be done in a controlled
-# way by setting EXPAND_ONLY_PREDEF to YES.
-
-MACRO_EXPANSION = NO
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-# then the macro expansion is limited to the macros specified with the
-# PREDEFINED and EXPAND_AS_DEFINED tags.
-
-EXPAND_ONLY_PREDEF = NO
-
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
-
-SEARCH_INCLUDES = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by
-# the preprocessor.
-
-INCLUDE_PATH =
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will
-# be used.
-
-INCLUDE_FILE_PATTERNS =
-
-# The PREDEFINED tag can be used to specify one or more macro names that
-# are defined before the preprocessor is started (similar to the -D option of
-# gcc). The argument of the tag is a list of macros of the form: name
-# or name=definition (no spaces). If the definition and the = are
-# omitted =1 is assumed. To prevent a macro definition from being
-# undefined via #undef or recursively expanded use the := operator
-# instead of the = operator.
-
-PREDEFINED =
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
-# this tag can be used to specify a list of macro names that should be expanded.
-# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition.
-
-EXPAND_AS_DEFINED =
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all function-like macros that are alone
-# on a line, have an all uppercase name, and do not end with a semicolon. Such
-# function macros are typically used for boiler-plate code, and will confuse
-# the parser if not removed.
-
-SKIP_FUNCTION_MACROS = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to external references
-#---------------------------------------------------------------------------
-
-# The TAGFILES option can be used to specify one or more tagfiles.
-# Optionally an initial location of the external documentation
-# can be added for each tagfile. The format of a tag file without
-# this location is as follows:
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths or
-# URLs. If a location is present for each tag, the installdox tool
-# does not have to be run to correct the links.
-# Note that each tag file must have a unique name
-# (where the name does NOT include the path)
-# If a tag file is not located in the directory in which doxygen
-# is run, you must also specify the path to the tagfile here.
-
-TAGFILES =
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
-
-GENERATE_TAGFILE =
-
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
-
-ALLEXTERNALS = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
-
-EXTERNAL_GROUPS = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
-
-PERL_PATH = /usr/bin/perl
-
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option is superseded by the HAVE_DOT option below. This is only a
-# fallback. It is recommended to install and use dot, since it yields more
-# powerful graphs.
-
-CLASS_DIAGRAMS = YES
-
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
-
-HIDE_UNDOC_RELATIONS = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
-
-HAVE_DOT = NO
-
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# the CLASS_DIAGRAMS tag to NO.
-
-CLASS_GRAPH = YES
-
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
-
-COLLABORATION_GRAPH = YES
-
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for groups, showing the direct groups dependencies
-
-GROUP_GRAPHS = YES
-
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
-# Language.
-
-UML_LOOK = YES
-
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
-
-TEMPLATE_RELATIONS = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
-
-INCLUDE_GRAPH = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
-
-INCLUDED_BY_GRAPH = YES
-
-# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will
-# generate a call dependency graph for every global function or class method.
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command.
-
-CALL_GRAPH = YES
-
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will graphical hierarchy of all classes instead of a textual one.
-
-GRAPHICAL_HIERARCHY = YES
-
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
-# then doxygen will show the dependencies a directory has on other directories
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
-
-DIRECTORY_GRAPH = YES
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are png, jpg, or gif
-# If left blank png will be used.
-
-DOT_IMAGE_FORMAT = png
-
-# The tag DOT_PATH can be used to specify the path where the dot tool can be
-# found. If left blank, it is assumed the dot tool can be found in the path.
-
-DOT_PATH =
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
-# \dotfile command).
-
-DOTFILE_DIRS =
-
-# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_WIDTH = 1024
-
-# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_HEIGHT = 1024
-
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
-# graphs generated by dot. A depth value of 3 means that only nodes reachable
-# from the root by following a path via at most 3 edges will be shown. Nodes
-# that lay further from the root node will be omitted. Note that setting this
-# option to 1 or 2 may greatly reduce the computation time needed for large
-# code bases. Also note that a graph may be further truncated if the graph's
-# image dimensions are not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH
-# and MAX_DOT_GRAPH_HEIGHT). If 0 is used for the depth value (the default),
-# the graph is not depth-constrained.
-
-MAX_DOT_GRAPH_DEPTH = 0
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, which results in a white background.
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-
-DOT_TRANSPARENT = NO
-
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
-# files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10)
-# support this, this feature is disabled by default.
-
-DOT_MULTI_TARGETS = NO
-
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
-# generate a legend page explaining the meaning of the various boxes and
-# arrows in the dot generated graphs.
-
-GENERATE_LEGEND = YES
-
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
-# remove the intermediate dot files that are used to generate
-# the various graphs.
-
-DOT_CLEANUP = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine
-#---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be
-# used. If set to NO the values of all tags below this one will be ignored.
-
-SEARCHENGINE = NO
diff --git a/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile.full b/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile.full
deleted file mode 100644
index dbb197ef373c5a9ba703c1bc339d309616c2e90a..0000000000000000000000000000000000000000
--- a/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile.full
+++ /dev/null
@@ -1,1237 +0,0 @@
-# Doxyfile 1.4.6
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
-#
-# All text after a hash (#) is considered a comment and will be ignored
-# The format is:
-# TAG = value [value, ...]
-# For lists items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
-# by quotes) that should identify the project.
-
-PROJECT_NAME = MOOSE
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
-
-PROJECT_NUMBER =
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
-
-OUTPUT_DIRECTORY = ./Docs/developer
-
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-# 4096 sub-directories (in 2 levels) under the output directory of each output
-# format and will distribute the generated files over these directories.
-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
-
-CREATE_SUBDIRS = NO
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish,
-# Dutch, Finnish, French, German, Greek, Hungarian, Italian, Japanese,
-# Japanese-en (Japanese with English messages), Korean, Korean-en, Norwegian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish,
-# Swedish, and Ukrainian.
-
-OUTPUT_LANGUAGE = English
-
-# This tag can be used to specify the encoding used in the generated output.
-# The encoding is not always determined by the language that is chosen,
-# but also whether or not the output is meant for Windows or non-Windows users.
-# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES
-# forces the Windows encoding (this is the default for the Windows binary),
-# whereas setting the tag to NO uses a Unix-style encoding (the default for
-# all platforms other than Windows).
-
-USE_WINDOWS_ENCODING = NO
-
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
-
-BRIEF_MEMBER_DESC = YES
-
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
-# brief descriptions will be completely suppressed.
-
-REPEAT_BRIEF = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator
-# that is used to form the text in various listings. Each string
-# in this list, if found as the leading text of the brief description, will be
-# stripped from the text and the result after processing the whole list, is
-# used as the annotated text. Otherwise, the brief description is used as-is.
-# If left blank, the following values are used ("$name" is automatically
-# replaced with the name of the entity): "The $name class" "The $name widget"
-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
-
-ABBREVIATE_BRIEF =
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
-# description.
-
-ALWAYS_DETAILED_SEC = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-
-INLINE_INHERITED_MEMB = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-# path before files name in the file list and in the header files. If set
-# to NO the shortest path that makes the file name unique will be used.
-
-FULL_PATH_NAMES = YES
-
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
-
-STRIP_FROM_PATH =
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-# the path mentioned in the documentation of a class, which tells
-# the reader which header file to include in order to use a class.
-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
-
-STRIP_FROM_INC_PATH =
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful is your file systems
-# doesn't support long names like on DOS, Mac, or CD-ROM.
-
-SHORT_NAMES = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like the Qt-style comments (thus requiring an
-# explicit @brief command for a brief description.
-
-JAVADOC_AUTOBRIEF = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
-# description. Set this tag to YES if you prefer the old behaviour instead.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the DETAILS_AT_TOP tag is set to YES then Doxygen
-# will output the detailed description near the top, like JavaDoc.
-# If set to NO, the detailed description appears after the member
-# documentation.
-
-DETAILS_AT_TOP = NO
-
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
-
-INHERIT_DOCS = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
-
-SEPARATE_MEMBER_PAGES = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
-
-TAB_SIZE = 4
-
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
-
-ALIASES =
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
-
-OPTIMIZE_OUTPUT_FOR_C = NO
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for Java.
-# For instance, namespaces will be presented as packages, qualified scopes
-# will look different, etc.
-
-OPTIMIZE_OUTPUT_JAVA = NO
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to
-# include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also make the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-
-BUILTIN_STL_SUPPORT = YES
-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
-# all members of a group must be documented explicitly.
-
-DISTRIBUTE_GROUP_DOC = NO
-
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
-
-SUBGROUPING = YES
-
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
-EXTRACT_ALL = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
-
-EXTRACT_PRIVATE = NO
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
-
-EXTRACT_STATIC = NO
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
-EXTRACT_LOCAL_METHODS = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_MEMBERS = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS = NO
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
-
-HIDE_IN_BODY_DOCS = NO
-
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
-
-INTERNAL_DOCS = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
-
-CASE_SENSE_NAMES = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
-
-HIDE_SCOPE_NAMES = NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
-
-SHOW_INCLUDE_FILES = YES
-
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
-
-INLINE_INFO = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
-
-SORT_MEMBER_DOCS = YES
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
-
-SORT_BRIEF_DOCS = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
-
-SORT_BY_SCOPE_NAME = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
-
-GENERATE_TODOLIST = YES
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
-
-GENERATE_TESTLIST = YES
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
-
-GENERATE_BUGLIST = YES
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
-
-GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
-
-ENABLED_SECTIONS =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or define consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and defines in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
-
-MAX_INITIALIZER_LINES = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
-# list will mention the files that were used to generate the documentation.
-
-SHOW_USED_FILES = YES
-
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES = NO
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from the
-# version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
-
-FILE_VERSION_FILTER =
-
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
-
-QUIET = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
-
-WARNINGS = YES
-
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
-
-WARN_IF_UNDOCUMENTED = YES
-
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
-
-WARN_IF_DOC_ERROR = YES
-
-# This WARN_NO_PARAMDOC option can be abled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
-
-WARN_NO_PARAMDOC = NO
-
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
-
-WARN_FORMAT = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
-
-WARN_LOGFILE =
-
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
-
-INPUT = ./Docs ./basecode ./biophysics ./builtins ./device ./geom ./hsolve ./kinetics ./ksolve ./manager ./mesh ./msg ./randnum ./sbml ./scheduling ./shell ./signeur ./smol ./testReduce ./threadTests ./utility
-
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
-
-FILE_PATTERNS =
-
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
-
-RECURSIVE = YES
-
-# The EXCLUDE tag can be used to specify files and/or directories that should
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-
-EXCLUDE =
-
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
-# directories that are symbolic links (a Unix filesystem feature) are excluded
-# from the input.
-
-EXCLUDE_SYMLINKS = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
-
-EXCLUDE_PATTERNS = *.py */.svn/*
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
-
-EXAMPLE_PATH =
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
-
-EXAMPLE_PATTERNS =
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
-
-EXAMPLE_RECURSIVE = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
-
-IMAGE_PATH = ./Docs/images
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output. If FILTER_PATTERNS is specified, this tag will be
-# ignored.
-
-INPUT_FILTER =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
-# is applied to all files.
-
-FILTER_PATTERNS =
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
-
-FILTER_SOURCE_FILES = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
-
-SOURCE_BROWSER = NO
-
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
-
-INLINE_SOURCES = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C and C++ comments will always remain visible.
-
-STRIP_CODE_COMMENTS = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES (the default)
-# then for each documented function all documented
-# functions referencing it will be listed.
-
-REFERENCED_BY_RELATION = YES
-
-# If the REFERENCES_RELATION tag is set to YES (the default)
-# then for each documented function all documented entities
-# called/used by that function will be listed.
-
-REFERENCES_RELATION = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
-
-USE_HTAGS = NO
-
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
-
-VERBATIM_HEADERS = YES
-
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
-
-ALPHABETICAL_INDEX = NO
-
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
-
-COLS_IN_ALPHA_INDEX = 5
-
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
-
-IGNORE_PREFIX =
-
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
-
-GENERATE_HTML = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
-
-HTML_OUTPUT = html
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
-
-HTML_FILE_EXTENSION = .html
-
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header.
-
-HTML_HEADER =
-
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
-
-HTML_FOOTER =
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# stylesheet in the HTML output directory as well, or it will be erased!
-
-HTML_STYLESHEET =
-
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS = YES
-
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compressed HTML help file (.chm)
-# of the generated HTML documentation.
-
-GENERATE_HTMLHELP = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
-# written to the html output directory.
-
-CHM_FILE =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
-
-HHC_LOCATION =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
-
-GENERATE_CHI = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
-
-BINARY_TOC = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
-
-TOC_EXPAND = NO
-
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
-# top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it.
-
-DISABLE_INDEX = NO
-
-# This tag can be used to set the number of enum values (range [1..20])
-# that doxygen will group on one line in the generated HTML documentation.
-
-ENUM_VALUES_PER_LINE = 4
-
-# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
-# generated containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
-# probably better off using the HTML help feature.
-
-GENERATE_TREEVIEW = NO
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
-
-TREEVIEW_WIDTH = 250
-
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
-
-GENERATE_LATEX = NO
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
-
-LATEX_OUTPUT = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-
-LATEX_CMD_NAME = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
-
-MAKEINDEX_CMD_NAME = makeindex
-
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_LATEX = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, a4wide, letter, legal and
-# executive. If left blank a4wide will be used.
-
-PAPER_TYPE = a4wide
-
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
-
-EXTRA_PACKAGES =
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
-
-LATEX_HEADER =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
-
-PDF_HYPERLINKS = NO
-
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
-# higher quality PDF documentation.
-
-USE_PDFLATEX = NO
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
-
-LATEX_BATCHMODE = NO
-
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
-
-LATEX_HIDE_INDICES = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
-
-GENERATE_RTF = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
-
-RTF_OUTPUT = rtf
-
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_RTF = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
-
-RTF_HYPERLINKS = NO
-
-# Load stylesheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
-
-RTF_STYLESHEET_FILE =
-
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
-
-RTF_EXTENSIONS_FILE =
-
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
-
-GENERATE_MAN = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
-
-MAN_OUTPUT = man
-
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
-
-MAN_EXTENSION = .3
-
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
-
-MAN_LINKS = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
-
-GENERATE_XML = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
-
-XML_OUTPUT = xml
-
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_SCHEMA =
-
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_DTD =
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
-
-XML_PROGRAMLISTING = YES
-
-#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
-
-GENERATE_AUTOGEN_DEF = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
-
-GENERATE_PERLMOD = NO
-
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
-
-PERLMOD_LATEX = NO
-
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader. This is useful
-# if you want to understand what is going on. On the other hand, if this
-# tag is set to NO the size of the Perl module output will be much smaller
-# and Perl will parse it just the same.
-
-PERLMOD_PRETTY = YES
-
-# The names of the make variables in the generated doxyrules.make file
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-# This is useful so different doxyrules.make files included by the same
-# Makefile don't overwrite each other's variables.
-
-PERLMOD_MAKEVAR_PREFIX =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
-#---------------------------------------------------------------------------
-
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-# evaluate all C-preprocessor directives found in the sources and include
-# files.
-
-ENABLE_PREPROCESSING = YES
-
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-# names in the source code. If set to NO (the default) only conditional
-# compilation will be performed. Macro expansion can be done in a controlled
-# way by setting EXPAND_ONLY_PREDEF to YES.
-
-MACRO_EXPANSION = NO
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-# then the macro expansion is limited to the macros specified with the
-# PREDEFINED and EXPAND_AS_DEFINED tags.
-
-EXPAND_ONLY_PREDEF = NO
-
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
-
-SEARCH_INCLUDES = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by
-# the preprocessor.
-
-INCLUDE_PATH =
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will
-# be used.
-
-INCLUDE_FILE_PATTERNS =
-
-# The PREDEFINED tag can be used to specify one or more macro names that
-# are defined before the preprocessor is started (similar to the -D option of
-# gcc). The argument of the tag is a list of macros of the form: name
-# or name=definition (no spaces). If the definition and the = are
-# omitted =1 is assumed. To prevent a macro definition from being
-# undefined via #undef or recursively expanded use the := operator
-# instead of the = operator.
-
-PREDEFINED =
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
-# this tag can be used to specify a list of macro names that should be expanded.
-# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition.
-
-EXPAND_AS_DEFINED =
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all function-like macros that are alone
-# on a line, have an all uppercase name, and do not end with a semicolon. Such
-# function macros are typically used for boiler-plate code, and will confuse
-# the parser if not removed.
-
-SKIP_FUNCTION_MACROS = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to external references
-#---------------------------------------------------------------------------
-
-# The TAGFILES option can be used to specify one or more tagfiles.
-# Optionally an initial location of the external documentation
-# can be added for each tagfile. The format of a tag file without
-# this location is as follows:
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths or
-# URLs. If a location is present for each tag, the installdox tool
-# does not have to be run to correct the links.
-# Note that each tag file must have a unique name
-# (where the name does NOT include the path)
-# If a tag file is not located in the directory in which doxygen
-# is run, you must also specify the path to the tagfile here.
-
-TAGFILES =
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
-
-GENERATE_TAGFILE =
-
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
-
-ALLEXTERNALS = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
-
-EXTERNAL_GROUPS = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
-
-PERL_PATH = /usr/bin/perl
-
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option is superseded by the HAVE_DOT option below. This is only a
-# fallback. It is recommended to install and use dot, since it yields more
-# powerful graphs.
-
-CLASS_DIAGRAMS = YES
-
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
-
-HIDE_UNDOC_RELATIONS = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
-
-HAVE_DOT = YES
-
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# the CLASS_DIAGRAMS tag to NO.
-
-CLASS_GRAPH = YES
-
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
-
-COLLABORATION_GRAPH = YES
-
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for groups, showing the direct groups dependencies
-
-GROUP_GRAPHS = YES
-
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
-# Language.
-
-UML_LOOK = YES
-
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
-
-TEMPLATE_RELATIONS = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
-
-INCLUDE_GRAPH = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
-
-INCLUDED_BY_GRAPH = YES
-
-# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will
-# generate a call dependency graph for every global function or class method.
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command.
-
-CALL_GRAPH = YES
-
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will graphical hierarchy of all classes instead of a textual one.
-
-GRAPHICAL_HIERARCHY = YES
-
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
-# then doxygen will show the dependencies a directory has on other directories
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
-
-DIRECTORY_GRAPH = YES
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are png, jpg, or gif
-# If left blank png will be used.
-
-DOT_IMAGE_FORMAT = png
-
-# The tag DOT_PATH can be used to specify the path where the dot tool can be
-# found. If left blank, it is assumed the dot tool can be found in the path.
-
-DOT_PATH =
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
-# \dotfile command).
-
-DOTFILE_DIRS =
-
-# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_WIDTH = 1024
-
-# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_HEIGHT = 1024
-
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
-# graphs generated by dot. A depth value of 3 means that only nodes reachable
-# from the root by following a path via at most 3 edges will be shown. Nodes
-# that lay further from the root node will be omitted. Note that setting this
-# option to 1 or 2 may greatly reduce the computation time needed for large
-# code bases. Also note that a graph may be further truncated if the graph's
-# image dimensions are not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH
-# and MAX_DOT_GRAPH_HEIGHT). If 0 is used for the depth value (the default),
-# the graph is not depth-constrained.
-
-MAX_DOT_GRAPH_DEPTH = 0
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, which results in a white background.
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-
-DOT_TRANSPARENT = NO
-
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
-# files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10)
-# support this, this feature is disabled by default.
-
-DOT_MULTI_TARGETS = NO
-
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
-# generate a legend page explaining the meaning of the various boxes and
-# arrows in the dot generated graphs.
-
-GENERATE_LEGEND = YES
-
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
-# remove the intermediate dot files that are used to generate
-# the various graphs.
-
-DOT_CLEANUP = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine
-#---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be
-# used. If set to NO the values of all tags below this one will be ignored.
-
-SEARCHENGINE = NO
diff --git a/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile.intermediate b/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile.intermediate
deleted file mode 100644
index 8b7c7d8c6c5a89d2e1c6b8aa37e3133dc3dc3ad8..0000000000000000000000000000000000000000
--- a/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile.intermediate
+++ /dev/null
@@ -1,1237 +0,0 @@
-# Doxyfile 1.4.6
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
-#
-# All text after a hash (#) is considered a comment and will be ignored
-# The format is:
-# TAG = value [value, ...]
-# For lists items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
-# by quotes) that should identify the project.
-
-PROJECT_NAME = MOOSE
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
-
-PROJECT_NUMBER =
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
-
-OUTPUT_DIRECTORY = ./Docs/developer
-
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-# 4096 sub-directories (in 2 levels) under the output directory of each output
-# format and will distribute the generated files over these directories.
-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
-
-CREATE_SUBDIRS = NO
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish,
-# Dutch, Finnish, French, German, Greek, Hungarian, Italian, Japanese,
-# Japanese-en (Japanese with English messages), Korean, Korean-en, Norwegian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish,
-# Swedish, and Ukrainian.
-
-OUTPUT_LANGUAGE = English
-
-# This tag can be used to specify the encoding used in the generated output.
-# The encoding is not always determined by the language that is chosen,
-# but also whether or not the output is meant for Windows or non-Windows users.
-# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES
-# forces the Windows encoding (this is the default for the Windows binary),
-# whereas setting the tag to NO uses a Unix-style encoding (the default for
-# all platforms other than Windows).
-
-USE_WINDOWS_ENCODING = NO
-
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
-
-BRIEF_MEMBER_DESC = YES
-
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
-# brief descriptions will be completely suppressed.
-
-REPEAT_BRIEF = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator
-# that is used to form the text in various listings. Each string
-# in this list, if found as the leading text of the brief description, will be
-# stripped from the text and the result after processing the whole list, is
-# used as the annotated text. Otherwise, the brief description is used as-is.
-# If left blank, the following values are used ("$name" is automatically
-# replaced with the name of the entity): "The $name class" "The $name widget"
-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
-
-ABBREVIATE_BRIEF =
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
-# description.
-
-ALWAYS_DETAILED_SEC = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-
-INLINE_INHERITED_MEMB = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-# path before files name in the file list and in the header files. If set
-# to NO the shortest path that makes the file name unique will be used.
-
-FULL_PATH_NAMES = YES
-
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
-
-STRIP_FROM_PATH =
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-# the path mentioned in the documentation of a class, which tells
-# the reader which header file to include in order to use a class.
-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
-
-STRIP_FROM_INC_PATH =
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful is your file systems
-# doesn't support long names like on DOS, Mac, or CD-ROM.
-
-SHORT_NAMES = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like the Qt-style comments (thus requiring an
-# explicit @brief command for a brief description.
-
-JAVADOC_AUTOBRIEF = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
-# description. Set this tag to YES if you prefer the old behaviour instead.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the DETAILS_AT_TOP tag is set to YES then Doxygen
-# will output the detailed description near the top, like JavaDoc.
-# If set to NO, the detailed description appears after the member
-# documentation.
-
-DETAILS_AT_TOP = NO
-
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
-
-INHERIT_DOCS = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
-
-SEPARATE_MEMBER_PAGES = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
-
-TAB_SIZE = 4
-
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
-
-ALIASES =
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
-
-OPTIMIZE_OUTPUT_FOR_C = NO
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for Java.
-# For instance, namespaces will be presented as packages, qualified scopes
-# will look different, etc.
-
-OPTIMIZE_OUTPUT_JAVA = NO
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to
-# include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also make the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-
-BUILTIN_STL_SUPPORT = YES
-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
-# all members of a group must be documented explicitly.
-
-DISTRIBUTE_GROUP_DOC = NO
-
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
-
-SUBGROUPING = YES
-
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
-EXTRACT_ALL = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
-
-EXTRACT_PRIVATE = NO
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
-
-EXTRACT_STATIC = NO
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
-EXTRACT_LOCAL_METHODS = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_MEMBERS = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS = NO
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
-
-HIDE_IN_BODY_DOCS = NO
-
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
-
-INTERNAL_DOCS = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
-
-CASE_SENSE_NAMES = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
-
-HIDE_SCOPE_NAMES = NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
-
-SHOW_INCLUDE_FILES = YES
-
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
-
-INLINE_INFO = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
-
-SORT_MEMBER_DOCS = YES
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
-
-SORT_BRIEF_DOCS = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
-
-SORT_BY_SCOPE_NAME = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
-
-GENERATE_TODOLIST = YES
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
-
-GENERATE_TESTLIST = YES
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
-
-GENERATE_BUGLIST = YES
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
-
-GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
-
-ENABLED_SECTIONS =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or define consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and defines in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
-
-MAX_INITIALIZER_LINES = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
-# list will mention the files that were used to generate the documentation.
-
-SHOW_USED_FILES = YES
-
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES = NO
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from the
-# version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
-
-FILE_VERSION_FILTER =
-
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
-
-QUIET = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
-
-WARNINGS = YES
-
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
-
-WARN_IF_UNDOCUMENTED = YES
-
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
-
-WARN_IF_DOC_ERROR = YES
-
-# This WARN_NO_PARAMDOC option can be abled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
-
-WARN_NO_PARAMDOC = NO
-
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
-
-WARN_FORMAT = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
-
-WARN_LOGFILE =
-
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
-
-INPUT = ./Docs ./basecode ./biophysics ./builtins ./device ./geom ./hsolve ./kinetics ./ksolve ./manager ./mesh ./msg ./randnum ./sbml ./scheduling ./shell ./signeur ./smol ./testReduce ./threadTests ./utility
-
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
-
-FILE_PATTERNS =
-
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
-
-RECURSIVE = YES
-
-# The EXCLUDE tag can be used to specify files and/or directories that should
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-
-EXCLUDE =
-
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
-# directories that are symbolic links (a Unix filesystem feature) are excluded
-# from the input.
-
-EXCLUDE_SYMLINKS = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
-
-EXCLUDE_PATTERNS = *.py */.svn/*
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
-
-EXAMPLE_PATH =
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
-
-EXAMPLE_PATTERNS =
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
-
-EXAMPLE_RECURSIVE = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
-
-IMAGE_PATH = ./Docs/images
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output. If FILTER_PATTERNS is specified, this tag will be
-# ignored.
-
-INPUT_FILTER =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
-# is applied to all files.
-
-FILTER_PATTERNS =
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
-
-FILTER_SOURCE_FILES = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
-
-SOURCE_BROWSER = NO
-
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
-
-INLINE_SOURCES = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C and C++ comments will always remain visible.
-
-STRIP_CODE_COMMENTS = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES (the default)
-# then for each documented function all documented
-# functions referencing it will be listed.
-
-REFERENCED_BY_RELATION = YES
-
-# If the REFERENCES_RELATION tag is set to YES (the default)
-# then for each documented function all documented entities
-# called/used by that function will be listed.
-
-REFERENCES_RELATION = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
-
-USE_HTAGS = NO
-
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
-
-VERBATIM_HEADERS = YES
-
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
-
-ALPHABETICAL_INDEX = NO
-
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
-
-COLS_IN_ALPHA_INDEX = 5
-
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
-
-IGNORE_PREFIX =
-
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
-
-GENERATE_HTML = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
-
-HTML_OUTPUT = html
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
-
-HTML_FILE_EXTENSION = .html
-
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header.
-
-HTML_HEADER =
-
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
-
-HTML_FOOTER =
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# stylesheet in the HTML output directory as well, or it will be erased!
-
-HTML_STYLESHEET =
-
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS = YES
-
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compressed HTML help file (.chm)
-# of the generated HTML documentation.
-
-GENERATE_HTMLHELP = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
-# written to the html output directory.
-
-CHM_FILE =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
-
-HHC_LOCATION =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
-
-GENERATE_CHI = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
-
-BINARY_TOC = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
-
-TOC_EXPAND = NO
-
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
-# top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it.
-
-DISABLE_INDEX = NO
-
-# This tag can be used to set the number of enum values (range [1..20])
-# that doxygen will group on one line in the generated HTML documentation.
-
-ENUM_VALUES_PER_LINE = 4
-
-# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
-# generated containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
-# probably better off using the HTML help feature.
-
-GENERATE_TREEVIEW = NO
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
-
-TREEVIEW_WIDTH = 250
-
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
-
-GENERATE_LATEX = NO
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
-
-LATEX_OUTPUT = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-
-LATEX_CMD_NAME = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
-
-MAKEINDEX_CMD_NAME = makeindex
-
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_LATEX = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, a4wide, letter, legal and
-# executive. If left blank a4wide will be used.
-
-PAPER_TYPE = a4wide
-
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
-
-EXTRA_PACKAGES =
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
-
-LATEX_HEADER =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
-
-PDF_HYPERLINKS = NO
-
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
-# higher quality PDF documentation.
-
-USE_PDFLATEX = NO
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
-
-LATEX_BATCHMODE = NO
-
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
-
-LATEX_HIDE_INDICES = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
-
-GENERATE_RTF = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
-
-RTF_OUTPUT = rtf
-
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_RTF = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
-
-RTF_HYPERLINKS = NO
-
-# Load stylesheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
-
-RTF_STYLESHEET_FILE =
-
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
-
-RTF_EXTENSIONS_FILE =
-
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
-
-GENERATE_MAN = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
-
-MAN_OUTPUT = man
-
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
-
-MAN_EXTENSION = .3
-
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
-
-MAN_LINKS = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
-
-GENERATE_XML = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
-
-XML_OUTPUT = xml
-
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_SCHEMA =
-
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_DTD =
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
-
-XML_PROGRAMLISTING = YES
-
-#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
-
-GENERATE_AUTOGEN_DEF = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
-
-GENERATE_PERLMOD = NO
-
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
-
-PERLMOD_LATEX = NO
-
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader. This is useful
-# if you want to understand what is going on. On the other hand, if this
-# tag is set to NO the size of the Perl module output will be much smaller
-# and Perl will parse it just the same.
-
-PERLMOD_PRETTY = YES
-
-# The names of the make variables in the generated doxyrules.make file
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-# This is useful so different doxyrules.make files included by the same
-# Makefile don't overwrite each other's variables.
-
-PERLMOD_MAKEVAR_PREFIX =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
-#---------------------------------------------------------------------------
-
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-# evaluate all C-preprocessor directives found in the sources and include
-# files.
-
-ENABLE_PREPROCESSING = YES
-
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-# names in the source code. If set to NO (the default) only conditional
-# compilation will be performed. Macro expansion can be done in a controlled
-# way by setting EXPAND_ONLY_PREDEF to YES.
-
-MACRO_EXPANSION = NO
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-# then the macro expansion is limited to the macros specified with the
-# PREDEFINED and EXPAND_AS_DEFINED tags.
-
-EXPAND_ONLY_PREDEF = NO
-
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
-
-SEARCH_INCLUDES = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by
-# the preprocessor.
-
-INCLUDE_PATH =
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will
-# be used.
-
-INCLUDE_FILE_PATTERNS =
-
-# The PREDEFINED tag can be used to specify one or more macro names that
-# are defined before the preprocessor is started (similar to the -D option of
-# gcc). The argument of the tag is a list of macros of the form: name
-# or name=definition (no spaces). If the definition and the = are
-# omitted =1 is assumed. To prevent a macro definition from being
-# undefined via #undef or recursively expanded use the := operator
-# instead of the = operator.
-
-PREDEFINED =
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
-# this tag can be used to specify a list of macro names that should be expanded.
-# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition.
-
-EXPAND_AS_DEFINED =
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all function-like macros that are alone
-# on a line, have an all uppercase name, and do not end with a semicolon. Such
-# function macros are typically used for boiler-plate code, and will confuse
-# the parser if not removed.
-
-SKIP_FUNCTION_MACROS = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to external references
-#---------------------------------------------------------------------------
-
-# The TAGFILES option can be used to specify one or more tagfiles.
-# Optionally an initial location of the external documentation
-# can be added for each tagfile. The format of a tag file without
-# this location is as follows:
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths or
-# URLs. If a location is present for each tag, the installdox tool
-# does not have to be run to correct the links.
-# Note that each tag file must have a unique name
-# (where the name does NOT include the path)
-# If a tag file is not located in the directory in which doxygen
-# is run, you must also specify the path to the tagfile here.
-
-TAGFILES =
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
-
-GENERATE_TAGFILE =
-
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
-
-ALLEXTERNALS = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
-
-EXTERNAL_GROUPS = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
-
-PERL_PATH = /usr/bin/perl
-
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option is superseded by the HAVE_DOT option below. This is only a
-# fallback. It is recommended to install and use dot, since it yields more
-# powerful graphs.
-
-CLASS_DIAGRAMS = YES
-
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
-
-HIDE_UNDOC_RELATIONS = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
-
-HAVE_DOT = YES
-
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# the CLASS_DIAGRAMS tag to NO.
-
-CLASS_GRAPH = YES
-
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
-
-COLLABORATION_GRAPH = YES
-
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for groups, showing the direct groups dependencies
-
-GROUP_GRAPHS = YES
-
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
-# Language.
-
-UML_LOOK = YES
-
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
-
-TEMPLATE_RELATIONS = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
-
-INCLUDE_GRAPH = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
-
-INCLUDED_BY_GRAPH = YES
-
-# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will
-# generate a call dependency graph for every global function or class method.
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command.
-
-CALL_GRAPH = NO
-
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will graphical hierarchy of all classes instead of a textual one.
-
-GRAPHICAL_HIERARCHY = YES
-
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
-# then doxygen will show the dependencies a directory has on other directories
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
-
-DIRECTORY_GRAPH = YES
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are png, jpg, or gif
-# If left blank png will be used.
-
-DOT_IMAGE_FORMAT = png
-
-# The tag DOT_PATH can be used to specify the path where the dot tool can be
-# found. If left blank, it is assumed the dot tool can be found in the path.
-
-DOT_PATH =
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
-# \dotfile command).
-
-DOTFILE_DIRS =
-
-# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_WIDTH = 1024
-
-# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_HEIGHT = 1024
-
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
-# graphs generated by dot. A depth value of 3 means that only nodes reachable
-# from the root by following a path via at most 3 edges will be shown. Nodes
-# that lay further from the root node will be omitted. Note that setting this
-# option to 1 or 2 may greatly reduce the computation time needed for large
-# code bases. Also note that a graph may be further truncated if the graph's
-# image dimensions are not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH
-# and MAX_DOT_GRAPH_HEIGHT). If 0 is used for the depth value (the default),
-# the graph is not depth-constrained.
-
-MAX_DOT_GRAPH_DEPTH = 0
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, which results in a white background.
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-
-DOT_TRANSPARENT = NO
-
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
-# files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10)
-# support this, this feature is disabled by default.
-
-DOT_MULTI_TARGETS = NO
-
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
-# generate a legend page explaining the meaning of the various boxes and
-# arrows in the dot generated graphs.
-
-GENERATE_LEGEND = YES
-
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
-# remove the intermediate dot files that are used to generate
-# the various graphs.
-
-DOT_CLEANUP = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine
-#---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be
-# used. If set to NO the values of all tags below this one will be ignored.
-
-SEARCHENGINE = NO
diff --git a/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile.minimal b/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile.minimal
deleted file mode 100644
index 73ede6e3c46e3c4d8770aea5f5e67aa77fd055bf..0000000000000000000000000000000000000000
--- a/moose-core/Docs/doxygen/doxy_1.4.6/Doxyfile.minimal
+++ /dev/null
@@ -1,1237 +0,0 @@
-# Doxyfile 1.4.6
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
-#
-# All text after a hash (#) is considered a comment and will be ignored
-# The format is:
-# TAG = value [value, ...]
-# For lists items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
-# by quotes) that should identify the project.
-
-PROJECT_NAME = MOOSE
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
-
-PROJECT_NUMBER =
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
-
-OUTPUT_DIRECTORY = ./Docs/developer
-
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-# 4096 sub-directories (in 2 levels) under the output directory of each output
-# format and will distribute the generated files over these directories.
-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
-
-CREATE_SUBDIRS = NO
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish,
-# Dutch, Finnish, French, German, Greek, Hungarian, Italian, Japanese,
-# Japanese-en (Japanese with English messages), Korean, Korean-en, Norwegian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish,
-# Swedish, and Ukrainian.
-
-OUTPUT_LANGUAGE = English
-
-# This tag can be used to specify the encoding used in the generated output.
-# The encoding is not always determined by the language that is chosen,
-# but also whether or not the output is meant for Windows or non-Windows users.
-# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES
-# forces the Windows encoding (this is the default for the Windows binary),
-# whereas setting the tag to NO uses a Unix-style encoding (the default for
-# all platforms other than Windows).
-
-USE_WINDOWS_ENCODING = NO
-
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
-
-BRIEF_MEMBER_DESC = YES
-
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
-# brief descriptions will be completely suppressed.
-
-REPEAT_BRIEF = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator
-# that is used to form the text in various listings. Each string
-# in this list, if found as the leading text of the brief description, will be
-# stripped from the text and the result after processing the whole list, is
-# used as the annotated text. Otherwise, the brief description is used as-is.
-# If left blank, the following values are used ("$name" is automatically
-# replaced with the name of the entity): "The $name class" "The $name widget"
-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
-
-ABBREVIATE_BRIEF =
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
-# description.
-
-ALWAYS_DETAILED_SEC = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-
-INLINE_INHERITED_MEMB = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-# path before files name in the file list and in the header files. If set
-# to NO the shortest path that makes the file name unique will be used.
-
-FULL_PATH_NAMES = YES
-
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
-
-STRIP_FROM_PATH =
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-# the path mentioned in the documentation of a class, which tells
-# the reader which header file to include in order to use a class.
-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
-
-STRIP_FROM_INC_PATH =
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful is your file systems
-# doesn't support long names like on DOS, Mac, or CD-ROM.
-
-SHORT_NAMES = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like the Qt-style comments (thus requiring an
-# explicit @brief command for a brief description.
-
-JAVADOC_AUTOBRIEF = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
-# description. Set this tag to YES if you prefer the old behaviour instead.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the DETAILS_AT_TOP tag is set to YES then Doxygen
-# will output the detailed description near the top, like JavaDoc.
-# If set to NO, the detailed description appears after the member
-# documentation.
-
-DETAILS_AT_TOP = NO
-
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
-
-INHERIT_DOCS = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
-
-SEPARATE_MEMBER_PAGES = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
-
-TAB_SIZE = 4
-
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
-
-ALIASES =
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
-
-OPTIMIZE_OUTPUT_FOR_C = NO
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for Java.
-# For instance, namespaces will be presented as packages, qualified scopes
-# will look different, etc.
-
-OPTIMIZE_OUTPUT_JAVA = NO
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to
-# include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also make the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-
-BUILTIN_STL_SUPPORT = YES
-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
-# all members of a group must be documented explicitly.
-
-DISTRIBUTE_GROUP_DOC = NO
-
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
-
-SUBGROUPING = YES
-
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
-EXTRACT_ALL = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
-
-EXTRACT_PRIVATE = NO
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
-
-EXTRACT_STATIC = NO
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
-EXTRACT_LOCAL_METHODS = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_MEMBERS = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS = NO
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
-
-HIDE_IN_BODY_DOCS = NO
-
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
-
-INTERNAL_DOCS = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
-
-CASE_SENSE_NAMES = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
-
-HIDE_SCOPE_NAMES = NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
-
-SHOW_INCLUDE_FILES = YES
-
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
-
-INLINE_INFO = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
-
-SORT_MEMBER_DOCS = YES
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
-
-SORT_BRIEF_DOCS = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
-
-SORT_BY_SCOPE_NAME = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
-
-GENERATE_TODOLIST = YES
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
-
-GENERATE_TESTLIST = YES
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
-
-GENERATE_BUGLIST = YES
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
-
-GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
-
-ENABLED_SECTIONS =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or define consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and defines in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
-
-MAX_INITIALIZER_LINES = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
-# list will mention the files that were used to generate the documentation.
-
-SHOW_USED_FILES = YES
-
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES = NO
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from the
-# version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
-
-FILE_VERSION_FILTER =
-
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
-
-QUIET = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
-
-WARNINGS = YES
-
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
-
-WARN_IF_UNDOCUMENTED = YES
-
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
-
-WARN_IF_DOC_ERROR = YES
-
-# This WARN_NO_PARAMDOC option can be abled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
-
-WARN_NO_PARAMDOC = NO
-
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
-
-WARN_FORMAT = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
-
-WARN_LOGFILE =
-
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
-
-INPUT = ./Docs ./basecode ./biophysics ./builtins ./device ./geom ./hsolve ./kinetics ./ksolve ./manager ./mesh ./msg ./randnum ./sbml ./scheduling ./shell ./signeur ./smol ./testReduce ./threadTests ./utility
-
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
-
-FILE_PATTERNS =
-
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
-
-RECURSIVE = YES
-
-# The EXCLUDE tag can be used to specify files and/or directories that should
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-
-EXCLUDE =
-
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
-# directories that are symbolic links (a Unix filesystem feature) are excluded
-# from the input.
-
-EXCLUDE_SYMLINKS = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
-
-EXCLUDE_PATTERNS = *.py */.svn/*
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
-
-EXAMPLE_PATH =
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
-
-EXAMPLE_PATTERNS =
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
-
-EXAMPLE_RECURSIVE = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
-
-IMAGE_PATH = ./Docs/images
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output. If FILTER_PATTERNS is specified, this tag will be
-# ignored.
-
-INPUT_FILTER =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
-# is applied to all files.
-
-FILTER_PATTERNS =
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
-
-FILTER_SOURCE_FILES = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
-
-SOURCE_BROWSER = NO
-
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
-
-INLINE_SOURCES = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C and C++ comments will always remain visible.
-
-STRIP_CODE_COMMENTS = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES (the default)
-# then for each documented function all documented
-# functions referencing it will be listed.
-
-REFERENCED_BY_RELATION = YES
-
-# If the REFERENCES_RELATION tag is set to YES (the default)
-# then for each documented function all documented entities
-# called/used by that function will be listed.
-
-REFERENCES_RELATION = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
-
-USE_HTAGS = NO
-
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
-
-VERBATIM_HEADERS = YES
-
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
-
-ALPHABETICAL_INDEX = NO
-
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
-
-COLS_IN_ALPHA_INDEX = 5
-
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
-
-IGNORE_PREFIX =
-
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
-
-GENERATE_HTML = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
-
-HTML_OUTPUT = html
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
-
-HTML_FILE_EXTENSION = .html
-
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header.
-
-HTML_HEADER =
-
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
-
-HTML_FOOTER =
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# stylesheet in the HTML output directory as well, or it will be erased!
-
-HTML_STYLESHEET =
-
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS = YES
-
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compressed HTML help file (.chm)
-# of the generated HTML documentation.
-
-GENERATE_HTMLHELP = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
-# written to the html output directory.
-
-CHM_FILE =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
-
-HHC_LOCATION =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
-
-GENERATE_CHI = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
-
-BINARY_TOC = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
-
-TOC_EXPAND = NO
-
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
-# top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it.
-
-DISABLE_INDEX = NO
-
-# This tag can be used to set the number of enum values (range [1..20])
-# that doxygen will group on one line in the generated HTML documentation.
-
-ENUM_VALUES_PER_LINE = 4
-
-# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
-# generated containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
-# probably better off using the HTML help feature.
-
-GENERATE_TREEVIEW = NO
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
-
-TREEVIEW_WIDTH = 250
-
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
-
-GENERATE_LATEX = NO
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
-
-LATEX_OUTPUT = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-
-LATEX_CMD_NAME = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
-
-MAKEINDEX_CMD_NAME = makeindex
-
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_LATEX = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, a4wide, letter, legal and
-# executive. If left blank a4wide will be used.
-
-PAPER_TYPE = a4wide
-
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
-
-EXTRA_PACKAGES =
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
-
-LATEX_HEADER =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
-
-PDF_HYPERLINKS = NO
-
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
-# higher quality PDF documentation.
-
-USE_PDFLATEX = NO
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
-
-LATEX_BATCHMODE = NO
-
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
-
-LATEX_HIDE_INDICES = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
-
-GENERATE_RTF = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
-
-RTF_OUTPUT = rtf
-
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_RTF = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
-
-RTF_HYPERLINKS = NO
-
-# Load stylesheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
-
-RTF_STYLESHEET_FILE =
-
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
-
-RTF_EXTENSIONS_FILE =
-
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
-
-GENERATE_MAN = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
-
-MAN_OUTPUT = man
-
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
-
-MAN_EXTENSION = .3
-
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
-
-MAN_LINKS = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
-
-GENERATE_XML = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
-
-XML_OUTPUT = xml
-
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_SCHEMA =
-
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_DTD =
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
-
-XML_PROGRAMLISTING = YES
-
-#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
-
-GENERATE_AUTOGEN_DEF = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
-
-GENERATE_PERLMOD = NO
-
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
-
-PERLMOD_LATEX = NO
-
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader. This is useful
-# if you want to understand what is going on. On the other hand, if this
-# tag is set to NO the size of the Perl module output will be much smaller
-# and Perl will parse it just the same.
-
-PERLMOD_PRETTY = YES
-
-# The names of the make variables in the generated doxyrules.make file
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-# This is useful so different doxyrules.make files included by the same
-# Makefile don't overwrite each other's variables.
-
-PERLMOD_MAKEVAR_PREFIX =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
-#---------------------------------------------------------------------------
-
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-# evaluate all C-preprocessor directives found in the sources and include
-# files.
-
-ENABLE_PREPROCESSING = YES
-
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-# names in the source code. If set to NO (the default) only conditional
-# compilation will be performed. Macro expansion can be done in a controlled
-# way by setting EXPAND_ONLY_PREDEF to YES.
-
-MACRO_EXPANSION = NO
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-# then the macro expansion is limited to the macros specified with the
-# PREDEFINED and EXPAND_AS_DEFINED tags.
-
-EXPAND_ONLY_PREDEF = NO
-
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
-
-SEARCH_INCLUDES = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by
-# the preprocessor.
-
-INCLUDE_PATH =
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will
-# be used.
-
-INCLUDE_FILE_PATTERNS =
-
-# The PREDEFINED tag can be used to specify one or more macro names that
-# are defined before the preprocessor is started (similar to the -D option of
-# gcc). The argument of the tag is a list of macros of the form: name
-# or name=definition (no spaces). If the definition and the = are
-# omitted =1 is assumed. To prevent a macro definition from being
-# undefined via #undef or recursively expanded use the := operator
-# instead of the = operator.
-
-PREDEFINED =
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
-# this tag can be used to specify a list of macro names that should be expanded.
-# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition.
-
-EXPAND_AS_DEFINED =
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all function-like macros that are alone
-# on a line, have an all uppercase name, and do not end with a semicolon. Such
-# function macros are typically used for boiler-plate code, and will confuse
-# the parser if not removed.
-
-SKIP_FUNCTION_MACROS = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to external references
-#---------------------------------------------------------------------------
-
-# The TAGFILES option can be used to specify one or more tagfiles.
-# Optionally an initial location of the external documentation
-# can be added for each tagfile. The format of a tag file without
-# this location is as follows:
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths or
-# URLs. If a location is present for each tag, the installdox tool
-# does not have to be run to correct the links.
-# Note that each tag file must have a unique name
-# (where the name does NOT include the path)
-# If a tag file is not located in the directory in which doxygen
-# is run, you must also specify the path to the tagfile here.
-
-TAGFILES =
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
-
-GENERATE_TAGFILE =
-
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
-
-ALLEXTERNALS = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
-
-EXTERNAL_GROUPS = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
-
-PERL_PATH = /usr/bin/perl
-
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option is superseded by the HAVE_DOT option below. This is only a
-# fallback. It is recommended to install and use dot, since it yields more
-# powerful graphs.
-
-CLASS_DIAGRAMS = YES
-
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
-
-HIDE_UNDOC_RELATIONS = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
-
-HAVE_DOT = NO
-
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# the CLASS_DIAGRAMS tag to NO.
-
-CLASS_GRAPH = YES
-
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
-
-COLLABORATION_GRAPH = YES
-
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for groups, showing the direct groups dependencies
-
-GROUP_GRAPHS = YES
-
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
-# Language.
-
-UML_LOOK = YES
-
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
-
-TEMPLATE_RELATIONS = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
-
-INCLUDE_GRAPH = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
-
-INCLUDED_BY_GRAPH = YES
-
-# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will
-# generate a call dependency graph for every global function or class method.
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command.
-
-CALL_GRAPH = YES
-
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will graphical hierarchy of all classes instead of a textual one.
-
-GRAPHICAL_HIERARCHY = YES
-
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
-# then doxygen will show the dependencies a directory has on other directories
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
-
-DIRECTORY_GRAPH = YES
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are png, jpg, or gif
-# If left blank png will be used.
-
-DOT_IMAGE_FORMAT = png
-
-# The tag DOT_PATH can be used to specify the path where the dot tool can be
-# found. If left blank, it is assumed the dot tool can be found in the path.
-
-DOT_PATH =
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
-# \dotfile command).
-
-DOTFILE_DIRS =
-
-# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_WIDTH = 1024
-
-# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_HEIGHT = 1024
-
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
-# graphs generated by dot. A depth value of 3 means that only nodes reachable
-# from the root by following a path via at most 3 edges will be shown. Nodes
-# that lay further from the root node will be omitted. Note that setting this
-# option to 1 or 2 may greatly reduce the computation time needed for large
-# code bases. Also note that a graph may be further truncated if the graph's
-# image dimensions are not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH
-# and MAX_DOT_GRAPH_HEIGHT). If 0 is used for the depth value (the default),
-# the graph is not depth-constrained.
-
-MAX_DOT_GRAPH_DEPTH = 0
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, which results in a white background.
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-
-DOT_TRANSPARENT = NO
-
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
-# files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10)
-# support this, this feature is disabled by default.
-
-DOT_MULTI_TARGETS = NO
-
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
-# generate a legend page explaining the meaning of the various boxes and
-# arrows in the dot generated graphs.
-
-GENERATE_LEGEND = YES
-
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
-# remove the intermediate dot files that are used to generate
-# the various graphs.
-
-DOT_CLEANUP = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine
-#---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be
-# used. If set to NO the values of all tags below this one will be ignored.
-
-SEARCHENGINE = NO
diff --git a/moose-core/Docs/doxygen/doxy_1.4.6/docgen b/moose-core/Docs/doxygen/doxy_1.4.6/docgen
deleted file mode 100755
index b6ad06d6236a9248bec4fe2569bfa6960a1ad224..0000000000000000000000000000000000000000
--- a/moose-core/Docs/doxygen/doxy_1.4.6/docgen
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/sh
-
-echo "###############################################################"
-echo "# Generating C++ Documentation #"
-echo "###############################################################"
-doxygen ./Doxyfile.full
-
-echo "##############################################################"
-echo "# Generating Python Documentation #"
-echo "##############################################################"
-
-( cd Docs/user/py && make html || true )
-
diff --git a/moose-core/Docs/generate-documentation b/moose-core/Docs/generate-documentation
deleted file mode 100755
index 8bc8649060a5bb49ec8b4a0b619ac6fe79ce0535..0000000000000000000000000000000000000000
--- a/moose-core/Docs/generate-documentation
+++ /dev/null
@@ -1,14 +0,0 @@
-echo "###############################################################"
-echo "# Generating C++ Documentation #"
-echo "###############################################################"
-#Files will be created in cpp/html with in `doxygen` folder
-orginal=$(echo `pwd`)
-cd doxygen
-doxygen Doxyfile
-cd $orginal
-
-echo "##############################################################"
-echo "# Generating Python Documentation #"
-echo "##############################################################"
-#Files will be created in _build/html `py` folder
-( cd user/py && make html || true )
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index fa7e32a22b4b31d5fb4ec33059c75d12f8a282a5..0000000000000000000000000000000000000000
--- a/moose-core/Docs/images/neuroncompartment.fig
+++ /dev/null
@@ -1,369 +0,0 @@
-#FIG 3.2 Produced by xfig version 3.2.5b
-Portrait
-Center
-Metric
-A4
-200.00
-Single
--2
-1200 2
-6 3465 3285 7155 5085
-6 3465 3285 7155 5085
-6 5805 3645 6165 4770
-6 5805 3671 6165 4770
-6 5805 4320 6165 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5805 4500 6165 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5895 4590 6075 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5985 4500 5985 4320
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5985 4590 5985 4770
--6
-# Resistor
-6 5880 3671 6060 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 5985 3686 5985 3824 5914 3847 6057 3893 5914 3939 6057 3984
- 5914 4030 6057 4076 5914 4122 6057 4167 5985 4190 5985 4329
--6
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 60.00 120.00
- 5850 4230 6120 3735
--6
-6 5040 3645 5400 4770
-# Resistor
-6 5115 3671 5295 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 5220 3686 5220 3824 5149 3847 5292 3893 5149 3939 5292 3984
- 5149 4030 5292 4076 5149 4122 5292 4167 5220 4190 5220 4329
--6
-6 5040 4320 5400 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5400 4590 5040 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5310 4500 5130 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5220 4590 5220 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5220 4500 5220 4320
--6
--6
-# Resistor
-6 3493 3585 4168 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 4153 3690 4015 3690 3992 3619 3946 3762 3900 3619 3855 3762
- 3809 3619 3763 3762 3717 3619 3672 3762 3649 3690 3510 3690
--6
-# Resistor
-6 6464 3585 7139 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 7124 3690 6986 3690 6963 3619 6917 3762 6871 3619 6826 3762
- 6780 3619 6734 3762 6688 3619 6643 3762 6620 3690 6481 3690
--6
-# Non-polar capacitor
-6 4237 3782 4745 4652
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 4269 4146 4730 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 4500 3800 4500 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 4500 4261 4500 4605
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 4269 4261 4730 4261
--6
-# Ground
-6 5265 4725 5580 5085
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 5409 4761 5409 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 5266 4903 5551 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 5337 4975 5480 4975
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 5380 5046 5451 5046
--6
-6 4435 3642 4570 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 4498 3689 28 28 4498 3689 4526 3689
--6
-6 5156 3642 5291 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5219 3689 28 28 5219 3689 5247 3689
--6
-6 5921 3642 6056 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5984 3689 28 28 5984 3689 6012 3689
--6
-6 5344 4723 5479 4813
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5407 4770 28 28 5407 4770 5435 4770
--6
-6 4798 3374 4933 3509
-1 3 0 1 0 7 1 0 20 0.000 1 0.0000 4858 3461 47 47 4858 3461 4906 3461
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4140 3690 6480 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4500 3825 4500 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4500 4590 4500 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4500 4770 5985 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4860 3510 4860 3690
-4 0 0 50 -1 0 12 0.0000 4 150 300 5355 4500 Em\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 5355 4050 Rm\001
-4 0 0 50 -1 0 12 0.0000 4 150 270 6165 4050 Gk\001
-4 0 0 50 -1 0 12 0.0000 4 150 240 6165 4590 Ek\001
-4 0 0 50 -1 0 12 0.0000 4 150 315 4635 4500 Cm\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 4955 3452 Vm\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 3664 3978 Ra/2\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 6637 3987 Ra/2\001
--6
-6 5158 4724 5293 4814
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5221 4771 28 28 5221 4771 5249 4771
--6
-6 4798 3641 4933 3731
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 4861 3688 28 28 4861 3688 4889 3688
--6
--6
-6 -360 3285 3330 5085
-6 -360 3285 3330 5085
-6 1980 3645 2340 4770
-6 1980 3671 2340 4770
-6 1980 4320 2340 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1980 4500 2340 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 2070 4590 2250 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 2160 4500 2160 4320
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 2160 4590 2160 4770
--6
-# Resistor
-6 2055 3671 2235 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 2160 3686 2160 3824 2089 3847 2232 3893 2089 3939 2232 3984
- 2089 4030 2232 4076 2089 4122 2232 4167 2160 4190 2160 4329
--6
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 60.00 120.00
- 2025 4230 2295 3735
--6
-6 1215 3645 1575 4770
-# Resistor
-6 1290 3671 1470 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 1395 3686 1395 3824 1324 3847 1467 3893 1324 3939 1467 3984
- 1324 4030 1467 4076 1324 4122 1467 4167 1395 4190 1395 4329
--6
-6 1215 4320 1575 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1575 4590 1215 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1485 4500 1305 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1395 4590 1395 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1395 4500 1395 4320
--6
--6
-# Resistor
-6 -332 3585 343 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 328 3690 190 3690 167 3619 121 3762 75 3619 30 3762
- -16 3619 -62 3762 -108 3619 -153 3762 -176 3690 -315 3690
--6
-# Resistor
-6 2639 3585 3314 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 3299 3690 3161 3690 3138 3619 3092 3762 3046 3619 3001 3762
- 2955 3619 2909 3762 2863 3619 2818 3762 2795 3690 2656 3690
--6
-# Non-polar capacitor
-6 412 3782 920 4652
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 444 4146 905 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 675 3800 675 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 675 4261 675 4605
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 444 4261 905 4261
--6
-# Ground
-6 1440 4725 1755 5085
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 1584 4761 1584 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 1441 4903 1726 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 1512 4975 1655 4975
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 1555 5046 1626 5046
--6
-6 610 3642 745 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 673 3689 28 28 673 3689 701 3689
--6
-6 1331 3642 1466 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1394 3689 28 28 1394 3689 1422 3689
--6
-6 2096 3642 2231 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 2159 3689 28 28 2159 3689 2187 3689
--6
-6 1519 4723 1654 4813
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1582 4770 28 28 1582 4770 1610 4770
--6
-6 973 3374 1108 3509
-1 3 0 1 0 7 1 0 20 0.000 1 0.0000 1033 3461 47 47 1033 3461 1081 3461
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 315 3690 2655 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 675 3825 675 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 675 4590 675 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 675 4770 2160 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1035 3510 1035 3690
-4 0 0 50 -1 0 12 0.0000 4 150 300 1530 4500 Em\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 1530 4050 Rm\001
-4 0 0 50 -1 0 12 0.0000 4 150 270 2340 4050 Gk\001
-4 0 0 50 -1 0 12 0.0000 4 150 240 2340 4590 Ek\001
-4 0 0 50 -1 0 12 0.0000 4 150 315 810 4500 Cm\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 1130 3452 Vm\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 -161 3978 Ra/2\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 2812 3987 Ra/2\001
--6
-6 1333 4724 1468 4814
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1396 4771 28 28 1396 4771 1424 4771
--6
-6 973 3641 1108 3731
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1036 3688 28 28 1036 3688 1064 3688
--6
--6
-6 7290 3285 10980 5085
-6 7290 3285 10980 5085
-6 9630 3645 9990 4770
-6 9630 3671 9990 4770
-6 9630 4320 9990 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9630 4500 9990 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9720 4590 9900 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9810 4500 9810 4320
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9810 4590 9810 4770
--6
-# Resistor
-6 9705 3671 9885 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 9810 3686 9810 3824 9739 3847 9882 3893 9739 3939 9882 3984
- 9739 4030 9882 4076 9739 4122 9882 4167 9810 4190 9810 4329
--6
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 60.00 120.00
- 9675 4230 9945 3735
--6
-6 8865 3645 9225 4770
-# Resistor
-6 8940 3671 9120 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 9045 3686 9045 3824 8974 3847 9117 3893 8974 3939 9117 3984
- 8974 4030 9117 4076 8974 4122 9117 4167 9045 4190 9045 4329
--6
-6 8865 4320 9225 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9225 4590 8865 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9135 4500 8955 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9045 4590 9045 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9045 4500 9045 4320
--6
--6
-# Resistor
-6 7318 3585 7993 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 7978 3690 7840 3690 7817 3619 7771 3762 7725 3619 7680 3762
- 7634 3619 7588 3762 7542 3619 7497 3762 7474 3690 7335 3690
--6
-# Resistor
-6 10289 3585 10964 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 10949 3690 10811 3690 10788 3619 10742 3762 10696 3619 10651 3762
- 10605 3619 10559 3762 10513 3619 10468 3762 10445 3690 10306 3690
--6
-# Non-polar capacitor
-6 8062 3782 8570 4652
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 8094 4146 8555 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 8325 3800 8325 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 8325 4261 8325 4605
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 8094 4261 8555 4261
--6
-# Ground
-6 9090 4725 9405 5085
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 9234 4761 9234 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 9091 4903 9376 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 9162 4975 9305 4975
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 9205 5046 9276 5046
--6
-6 8260 3642 8395 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 8323 3689 28 28 8323 3689 8351 3689
--6
-6 8981 3642 9116 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9044 3689 28 28 9044 3689 9072 3689
--6
-6 9746 3642 9881 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9809 3689 28 28 9809 3689 9837 3689
--6
-6 9169 4723 9304 4813
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9232 4770 28 28 9232 4770 9260 4770
--6
-6 8623 3374 8758 3509
-1 3 0 1 0 7 1 0 20 0.000 1 0.0000 8683 3461 47 47 8683 3461 8731 3461
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 7965 3690 10305 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 8325 3825 8325 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 8325 4590 8325 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 8325 4770 9810 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 8685 3510 8685 3690
-4 0 0 50 -1 0 12 0.0000 4 150 300 9180 4500 Em\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 9180 4050 Rm\001
-4 0 0 50 -1 0 12 0.0000 4 150 270 9990 4050 Gk\001
-4 0 0 50 -1 0 12 0.0000 4 150 240 9990 4590 Ek\001
-4 0 0 50 -1 0 12 0.0000 4 150 315 8460 4500 Cm\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 8780 3452 Vm\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 7489 3978 Ra/2\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 10462 3987 Ra/2\001
--6
-6 8983 4724 9118 4814
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9046 4771 28 28 9046 4771 9074 4771
--6
-6 8623 3641 8758 3731
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 8686 3688 28 28 8686 3688 8714 3688
--6
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 3285 3690 3510 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 7110 3690 7335 3690
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
- 3420 3240 7245 3240 7245 5130 3420 5130 3420 3240
diff --git a/moose-core/Docs/images/neuroncompartment.png b/moose-core/Docs/images/neuroncompartment.png
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diff --git a/moose-core/Docs/images/twoCells.png b/moose-core/Docs/images/twoCells.png
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diff --git a/moose-core/Docs/markdown/README.html b/moose-core/Docs/markdown/README.html
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index 7d88f439b1dd7615ff2e68ce6a7359a968eb271a..0000000000000000000000000000000000000000
--- a/moose-core/Docs/markdown/README.html
+++ /dev/null
@@ -1,613 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
- <title>Quick Introduction to Markdown</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta name="generator" content="pandoc" />
- <meta name="author" content="Niraj Dudani" />
- <meta name="date" content="January 2, 2013" />
- <style type="text/css">
- table.sourceCode, tr.sourceCode, td.lineNumbers, td.sourceCode, table.sourceCode pre { margin: 0; padding: 0; border: 0; vertical-align: baseline; border: none; }
- td.lineNumbers { border-right: 1px solid #AAAAAA; text-align: right; color: #AAAAAA; padding-right: 5px; padding-left: 5px; }
- td.sourceCode { padding-left: 5px; }
- pre.sourceCode { }
- pre.sourceCode span.Normal { }
- pre.sourceCode span.Keyword { color: #007020; font-weight: bold; }
- pre.sourceCode span.DataType { color: #902000; }
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- pre.sourceCode span.Char { color: #4070a0; }
- pre.sourceCode span.String { color: #4070a0; }
- pre.sourceCode span.Comment { color: #60a0b0; font-style: italic; }
- pre.sourceCode span.Others { color: #007020; }
- pre.sourceCode span.Alert { color: red; font-weight: bold; }
- pre.sourceCode span.Function { color: #06287e; }
- pre.sourceCode span.RegionMarker { }
- pre.sourceCode span.Error { color: red; font-weight: bold; }
- </style>
- <link rel="stylesheet" href="css/stylesheet.css" type="text/css" />
-</head>
-<body>
-
-<h1 class="title">Quick Introduction to Markdown</h1>
-
-<h2>
- Niraj Dudani
-</h2>
-
-<h2>January 2, 2013</h2>
-
-<div id="TOC"
-><ul
- ><li
- ><a href="#introduction"
- >Introduction</a
- ></li
- ><li
- ><a href="#converting-to-html"
- >Converting to HTML</a
- ></li
- ><li
- ><a href="#examples"
- >Examples</a
- ><ul
- ><li
- ><a href="#lists-emphasis-etc."
- >Lists, emphasis, etc.</a
- ></li
- ><li
- ><a href="#quoting-text-code-etc."
- >Quoting text, code, etc.</a
- ></li
- ><li
- ><a href="#linking-images-and-tables"
- >Linking, images and tables</a
- ></li
- ></ul
- ></li
- ><li
- ><a href="#conclusion"
- >Conclusion</a
- ></li
- ><li
- ><a href="#footnotes"
- >Footnotes</a
- ></li
- ></ul
- ></div
->
-<div id="introduction"
-><h1
- ><a href="#TOC"
- >Introduction</a
- ></h1
- ><p
- >This document is written in Markdown<sup
- ><a href="#fn1" class="footnoteRef" id="fnref1"
- >1</a
- ></sup
- >. Here is the philosophy behind this format:</p
- ><blockquote
- ><p
- >A Markdown-formatted document should be publishable as-is, as plain text, without looking like it’s been marked up with tags or formatting instructions.</p
- ></blockquote
- ><p
- >For MOOSE documentation, we use Pandoc<sup
- ><a href="#fn2" class="footnoteRef" id="fnref2"
- >2</a
- ></sup
- > to convert from Markdown to HTML. Pandoc adds some nice things to Markdown, like tables and footnotes.</p
- ></div
-><div id="converting-to-html"
-><h1
- ><a href="#TOC"
- >Converting to HTML</a
- ></h1
- ><p
- >To convert this document to HTML, run the command in the <code
- >build</code
- > script included in this directory. This command also requests <code
- >pandoc</code
- > to generate a table-of-contents for this document.</p
- ><p
- >To install <code
- >pandoc</code
- > on Ubuntu, simply issue:</p
- ><pre
- ><code
- >sudo apt-get install pandoc
-</code
- ></pre
- ></div
-><div id="examples"
-><h1
- ><a href="#TOC"
- >Examples</a
- ></h1
- ><p
- >In the following subsections, we look at a few examples.</p
- ><div id="lists-emphasis-etc."
- ><h2
- ><a href="#TOC"
- >Lists, emphasis, etc.</a
- ></h2
- ><p
- >This is a bullet-list of some things that Markdown can do:</p
- ><ul
- ><li
- ><p
- >This is <em
- >emphasis</em
- >.</p
- ></li
- ><li
- ><p
- >This is <strong
- >stronger emphasis</strong
- >.</p
- ></li
- ><li
- ><p
- >You can add <sup
- >superscript</sup
- > / <sub
- >subscript</sub
- > / <span style="text-decoration: line-through;"
- >strikeout</span
- >.</p
- ></li
- ><li
- ><p
- >You can add <code
- >verbatim text</code
- > inline. This is useful for <code
- >variables</code
- >, <code
- >functions()</code
- >, etc.</p
- ></li
- ></ul
- ></div
- ><div id="quoting-text-code-etc."
- ><h2
- ><a href="#TOC"
- >Quoting text, code, etc.</a
- ></h2
- ><p
- >To quote text, use <code
- >></code
- >, as in email:</p
- ><blockquote
- ><p
- ><strong
- >Rock Story</strong
- ><br
- />Â -- <em
- >Dik Browne</em
- ></p
- ><p
- >LE: What crazy mixed-up rocks!<br
- />HH: Quiet, stupid!</p
- ><p
- >HH: You're in a very special place... Full of age and mystery...<br
- />LE: No kidding!</p
- ><p
- >LE: <strong
- >Wow! Crazy!</strong
- > What is it?<br
- />HH: It's a monument!</p
- ><p
- >HH: Thousands of people slaved for years to drag those stones here and put them in place!<br
- />LE: Why?</p
- ><p
- >HH: For their leader! When you're a big shot, you do that so people will always remember you!<br
- />Â Â Â Â That's called <strong
- >immortality!</strong
- ><br
- />LE: <strong
- >Wow!</strong
- ></p
- ><p
- >LE: Who was he?<br
- />HH: Nobody knows...</p
- ></blockquote
- ><p
- >If you're lazy, a single <code
- >></code
- > is enough:</p
- ><blockquote
- ><p
- ><strong
- >The Purist</strong
- ><br
- />Â Â -- <em
- >Ogden Nash</em
- ><br
- /><br
- />I give you now Professor Twist,<br
- />A conscientious scientist,<br
- />Trustees exclaimed, "He never bungles!"<br
- />And sent him off to distant jungles.<br
- />Camped on a tropic riverside,<br
- />One day he missed his loving bride.<br
- />She had, the guide informed him later,<br
- />Been eaten by an alligator.<br
- />Professor Twist could not but smile.<br
- />"You mean," he said, "a crocodile."</p
- ></blockquote
- ><p
- >At any time,<br
- />end lines with<br
- />2 spaces<br
- />to retain<br
- />line-endings (as done in the examples above).</p
- ><p
- >Insert code using 4 spaces:</p
- ><pre
- ><code
- >echo "Sanitizing..."
-rm -rf /
-</code
- ></pre
- ><p
- >or a few tildes:</p
- ><table class="sourceCode"
- ><tr
- ><td class="lineNumbers" title="Click to toggle line numbers" onclick="with (this.firstChild.style) { display = (display == '') ? 'none' : '' }"
- ><pre
- >10<br
- />11<br
- />12<br
- />13<br
- />14</pre
- ></td
- ><td class="sourceCode"
- ><pre class="sourceCode python"
- ><code
- ><span class="Keyword DefinitionKeyword"
- >def</span
- ><span class="Normal NormalText"
- > </span
- ><span class="Normal"
- >factorial</span
- ><span class="Normal Operator"
- >(</span
- ><span class="Normal NormalText"
- > n </span
- ><span class="Normal Operator"
- >)</span
- ><span class="Normal NormalText"
- >:</span
- ><br
- /><span class="Normal NormalText"
- > </span
- ><span class="Keyword FlowControlKeyword"
- >if</span
- ><span class="Normal NormalText"
- > </span
- ><span class="Normal Operator"
- >(</span
- ><span class="Normal NormalText"
- > n </span
- ><span class="Normal Operator"
- ><=</span
- ><span class="Normal NormalText"
- > </span
- ><span class="DecVal Int"
- >1</span
- ><span class="Normal NormalText"
- > </span
- ><span class="Normal Operator"
- >)</span
- ><span class="Normal NormalText"
- >:</span
- ><br
- /><span class="Normal NormalText"
- > </span
- ><span class="Keyword FlowControlKeyword"
- >return</span
- ><span class="Normal NormalText"
- > </span
- ><span class="DecVal Int"
- >1</span
- ><br
- /><span class="Normal NormalText"
- > </span
- ><span class="Keyword FlowControlKeyword"
- >else</span
- ><span class="Normal NormalText"
- >:</span
- ><br
- /><span class="Normal NormalText"
- > </span
- ><span class="Keyword FlowControlKeyword"
- >return</span
- ><span class="Normal NormalText"
- > n </span
- ><span class="Normal Operator"
- >*</span
- ><span class="Normal NormalText"
- > </span
- ><span class="Normal"
- >factorial</span
- ><span class="Normal Operator"
- >(</span
- ><span class="Normal NormalText"
- > n </span
- ><span class="Normal Operator"
- >-</span
- ><span class="Normal NormalText"
- > </span
- ><span class="DecVal Int"
- >1</span
- ><span class="Normal NormalText"
- > </span
- ><span class="Normal Operator"
- >)</span
- ><br
- /></code
- ></pre
- ></td
- ></tr
- ></table
- ></div
- ><div id="linking-images-and-tables"
- ><h2
- ><a href="#TOC"
- >Linking, images and tables</a
- ></h2
- ><p
- >You can link to <a href="http://www.zombo.com/"
- >an external website</a
- >, or to <a href="#introduction"
- >a section</a
- > on the same page.</p
- ><p
- >You can insert images and have captions for them. Here an image has been sandwiched between 2 horizontal rules:</p
- ><hr
- /><div class="figure"
- ><img src="images/purkinje.png" title="You can add alt-text too!" alt="<em
->Purkinje cell in MOOSE</em
->"
- /><p class="caption"
- ><em
- >Purkinje cell in MOOSE</em
- ></p
- ></div
- ><hr
- /><p
- >Tables can have headers:</p
- ><table
- ><thead
- ><tr class="header"
- ><th align="right"
- >Right</th
- ><th align="left"
- >Left</th
- ><th align="center"
- >Center</th
- ><th align="left"
- >Default</th
- ></tr
- ></thead
- ><tbody
- ><tr class="odd"
- ><td align="right"
- >12</td
- ><td align="left"
- >12</td
- ><td align="center"
- >12</td
- ><td align="left"
- >12</td
- ></tr
- ><tr class="even"
- ><td align="right"
- >123</td
- ><td align="left"
- >123</td
- ><td align="center"
- >123</td
- ><td align="left"
- >123</td
- ></tr
- ><tr class="odd"
- ><td align="right"
- >1</td
- ><td align="left"
- >1</td
- ><td align="center"
- >1</td
- ><td align="left"
- >1</td
- ></tr
- ></tbody
- ></table
- ><p
- >or not:</p
- ><table
- ><tbody
- ><tr class="odd"
- ><td align="center"
- >♜</td
- ><td align="center"
- >♞</td
- ><td align="center"
- >â™</td
- ><td align="center"
- >â™›</td
- ><td align="center"
- >♚</td
- ><td align="center"
- >â™</td
- ><td align="center"
- >♞</td
- ><td align="center"
- >♜</td
- ></tr
- ><tr class="even"
- ><td align="center"
- >♟</td
- ><td align="center"
- >♟</td
- ><td align="center"
- >♟</td
- ><td align="center"
- >♟</td
- ><td align="center"
- >♟</td
- ><td align="center"
- >♟</td
- ><td align="center"
- >♟</td
- ><td align="center"
- >♟</td
- ></tr
- ><tr class="odd"
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ></tr
- ><tr class="even"
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ></tr
- ><tr class="odd"
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ></tr
- ><tr class="even"
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ><td align="center"
- >â—¼</td
- ><td align="center"
- >â—»</td
- ></tr
- ><tr class="odd"
- ><td align="center"
- >â™™</td
- ><td align="center"
- >â™™</td
- ><td align="center"
- >â™™</td
- ><td align="center"
- >â™™</td
- ><td align="center"
- >â™™</td
- ><td align="center"
- >â™™</td
- ><td align="center"
- >â™™</td
- ><td align="center"
- >â™™</td
- ></tr
- ><tr class="even"
- ><td align="center"
- >♖</td
- ><td align="center"
- >♘</td
- ><td align="center"
- >â™—</td
- ><td align="center"
- >♕</td
- ><td align="center"
- >â™”</td
- ><td align="center"
- >â™—</td
- ><td align="center"
- >♘</td
- ><td align="center"
- >â™–</td
- ></tr
- ></tbody
- ></table
- ></div
- ></div
-><div id="conclusion"
-><h1
- ><a href="#TOC"
- >Conclusion</a
- ></h1
- ><p
- >Markdown and Pandoc have many more features. For these, go to the links in the footnotes.</p
- ></div
-><div id="footnotes"
-><h1
- ><a href="#TOC"
- >Footnotes</a
- ></h1
- ></div
-><div class="footnotes"
-><hr
- /><ol
- ><li id="fn1"
- ><p
- ><a href="http://daringfireball.net/projects/markdown/basics"
- >Link to Markdown website</a
- > <a href="#fnref1" class="footnoteBackLink" title="Jump back to footnote 1">↩</a></p
- ></li
- ><li id="fn2"
- ><p
- ><a href="http://johnmacfarlane.net/pandoc/README.html"
- >Link to Pandoc website</a
- > <a href="#fnref2" class="footnoteBackLink" title="Jump back to footnote 2">↩</a></p
- ></li
- ></ol
- ></div
->
-</body>
-</html>
-
diff --git a/moose-core/Docs/markdown/README.markdown b/moose-core/Docs/markdown/README.markdown
deleted file mode 100644
index b7eadfc11478d38c0db632cdd9a965adcb783f8a..0000000000000000000000000000000000000000
--- a/moose-core/Docs/markdown/README.markdown
+++ /dev/null
@@ -1,152 +0,0 @@
-% Quick Introduction to Markdown
-% Niraj Dudani
-% January 2, 2013
-
-# Introduction
-
-This document is written in Markdown[^markdown]. Here is the philosophy behind
-this format:
-
-> A Markdown-formatted document should be publishable as-is, as plain text,
-> without looking like it’s been marked up with tags or formatting
-> instructions.
-
-For MOOSE documentation, we use Pandoc[^pandoc] to convert from Markdown to
-HTML. Pandoc adds some nice things to Markdown, like tables and footnotes.
-
-# Converting to HTML
-
-To convert this document to HTML, run the command in the `build` script included
-in this directory. This command also requests `pandoc` to generate a
-table-of-contents for this document.
-
-To install `pandoc` on Ubuntu, simply issue:
-
- sudo apt-get install pandoc
-
-# Examples
-
-In the following subsections, we look at a few examples.
-
-## Lists, emphasis, etc.
-
-This is a bullet-list of some things that Markdown can do:
-
- - This is *emphasis*.
-
- - This is **stronger emphasis**.
-
- - You can add ^superscript^ / ~subscript~ / ~~strikeout~~.
-
- - You can add `verbatim text` inline. This is useful for `variables`,
- `functions()`, etc.
-
-## Quoting text, code, etc.
-
-To quote text, use `>`, as in email:
-
-> **Rock Story**
-> \ -- *Dik Browne*
->
-> LE: What crazy mixed-up rocks!
-> HH: Quiet, stupid!
->
-> HH: You're in a very special place... Full of age and mystery...
-> LE: No kidding!
->
-> LE: **Wow! Crazy!** What is it?
-> HH: It's a monument!
->
-> HH: Thousands of people slaved for years to drag those stones here and put
-> them in place!
-> LE: Why?
->
-> HH: For their leader! When you're a big shot, you do that so people will
-> always remember you!
-> \ \ \ \ That's called **immortality!**
-> LE: **Wow!**
->
-> LE: Who was he?
-> HH: Nobody knows...
-
- If you're lazy, a single `>` is enough:
-
-> **The Purist**
-\ \ -- *Ogden Nash*
-\
-I give you now Professor Twist,
-A conscientious scientist,
-Trustees exclaimed, "He never bungles!"
-And sent him off to distant jungles.
-Camped on a tropic riverside,
-One day he missed his loving bride.
-She had, the guide informed him later,
-Been eaten by an alligator.
-Professor Twist could not but smile.
-"You mean," he said, "a crocodile."
-
-At any time,
-end lines with
-2 spaces
-to retain
-line-endings (as done in the examples above).
-
-Insert code using 4 spaces:
-
- echo "Sanitizing..."
- rm -rf /
-
-or a few tildes:
-
-~~~~~~~~~~{.python .numberLines startFrom="10"}
-def factorial( n ):
- if ( n <= 1 ):
- return 1
- else:
- return n * factorial( n - 1 )
-~~~~~~~~~~
-
-## Linking, images and tables
-
-You can link to [an external website](http://www.zombo.com/), or to
-[a section](#introduction) on the same page.
-
-You can insert images and have captions for them. Here an image has been
-sandwiched between 2 horizontal rules:
-
-**********
-
-
-
-**********
-
-Tables can have headers:
-
- Right Left Center Default
-------- ------ ---------- -------
- 12 12 12 12
- 123 123 123 123
- 1 1 1 1
-
-or not:
-
------ ----- ----- ----- ----- ----- ----- -----
- ♜ ♞ ♠♛ ♚ ♠♞ ♜
- ♟ ♟ ♟ ♟ ♟ ♟ ♟ ♟
- â—» â—¼ â—» â—¼ â—» â—¼ â—» â—¼
- â—¼ â—» â—¼ â—» â—¼ â—» â—¼ â—»
- â—» â—¼ â—» â—¼ â—» â—¼ â—» â—¼
- â—¼ â—» â—¼ â—» â—¼ â—» â—¼ â—»
- â™™ â™™ â™™ â™™ â™™ â™™ â™™ â™™
- ♖ ♘ ♗ ♕ ♔ ♗ ♘ ♖
------ ----- ----- ----- ----- ----- ----- -----
-
-# Conclusion
-
-Markdown and Pandoc have many more features. For these, go to the links
-in the footnotes.
-
-# Footnotes
-
-[^markdown]: [Link to Markdown website](http://daringfireball.net/projects/markdown/basics)
-[^pandoc]: [Link to Pandoc website](http://johnmacfarlane.net/pandoc/README.html)
diff --git a/moose-core/Docs/markdown/build b/moose-core/Docs/markdown/build
deleted file mode 100755
index 3f250d620406ab41be2942a7762405eb153288d1..0000000000000000000000000000000000000000
--- a/moose-core/Docs/markdown/build
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/sh
-
-echo "[ Generating HTML ]"
-echo "README.markdown -> README.html"
-
-pandoc \
- --toc \
- -c css/stylesheet.css \
- README.markdown -o README.html
diff --git a/moose-core/Docs/markdown/css/stylesheet.css b/moose-core/Docs/markdown/css/stylesheet.css
deleted file mode 100644
index c937ff53a6ad1983a0e4fe09dd62cbe9869ec041..0000000000000000000000000000000000000000
--- a/moose-core/Docs/markdown/css/stylesheet.css
+++ /dev/null
@@ -1,121 +0,0 @@
-body {
- margin: auto;
- padding-right: 1em;
- padding-left: 1em;
- color: black;
- font-family: Verdana, sans-serif;
- font-size: 100%;
- line-height: 140%;
- color: #333;
-}
-
-pre {
- background-color: #EFC;
- color: #333;
- line-height: 120%;
- border: 1px solid #AC9;
- border-left: none;
- border-right: none;
- max-width: 80em;
- color: #1111111;
- padding: 0.5em;
-}
-
-blockquote {
- border: 1px dotted gray;
- background-color: #ececec;
- max-width: 70em;
- font-family: monospace;
- color: #1111111;
- padding: 0.5em;
-}
-
-code {
- font-family: monospace;
-}
-
-h1 a, h2 a, h3 a, h4 a, h5 a {
- text-decoration: none;
- color: #7a5ada;
-}
-
-h1, h2, h3, h4, h5 {
- font-family: verdana;
- font-weight: bold;
- border-bottom: 1px dotted black;
- color: #7a5ada;
-}
-
-h1 {
- font-size: 130%;
-}
-
-h2 {
- font-size: 110%;
-}
-
-h3 {
- font-size: 95%;
-}
-
-h4 {
- font-size: 90%;
- font-style: italic;
-}
-
-h5 {
- font-size: 90%;
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- font-weight: bold;
- padding-top: 0.2em;
- padding-bottom: 0.2em;
- text-align: left;
- border: none;
-}
-
-dt code {
- font-weight: bold;
-}
-
-dd p {
- margin-top: 0;
-}
-
-#footer {
- padding-top: 1em;
- font-size: 70%;
- color: gray;
- text-align: center;
-}
-
-table {
- width: 20%;
- border: 1px solid #B099FF;
- border-collapse: collapse;
-}
-
-td {
- border: 1px solid #B099FF;
- padding: 4px;
-}
-
-th {
- color: white;
- background-color: #C5B3FF;
- border: 1px solid #B099FF;
-
- /* Padding: top-bottom and left-right */
- padding: 6px 4px;
-}
-
-tr:nth-child( odd ) {
- background-color: #FFFFFF;
-}
-
-tr:nth-child( even ) {
- background-color: #E7E0FF;
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diff --git a/moose-core/Docs/user/GUI/Kkit12Documentation.rst b/moose-core/Docs/user/GUI/Kkit12Documentation.rst
deleted file mode 100644
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--- a/moose-core/Docs/user/GUI/Kkit12Documentation.rst
+++ /dev/null
@@ -1,491 +0,0 @@
---------------
-
-Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI
-===============================================================
-
-Upinder Bhalla, Harsha Rani
-
-Feb 25 2016.
-
---------------
-
-- `Introduction <#introduction>`_
-
-- `**TODO** What are chemical kinetic
- models? <#todo-what-are-chemical-kinetic-models>`_
-
- - `Levels of model <#levels-of-model>`_
- - `Numerical methods <#numerical-methods>`_
-
-- `Using Kinetikit 12 <#using-kinetikit-12>`_
-
- - `Overview <#overview>`_
- - `Model layout and icons <#model-layout-and-icons>`_
-
- - `Compartment <#compartment>`_
- - `Pool <#pool>`_
- - `Buffered pools <#buffered-pools>`_
- - `Reaction <#reaction>`_
- - `Mass-action enzymes <#mass-action-enzymes>`_
- - `Michaelis-Menten Enzymes <#michaelis-menten-enzymes>`_
- - `Function <#function>`_
-
- - `Model operations <#model-operations>`_
- - `Model Building <#model-building>`_
-
-`Introduction <#TOC>`_
-----------------------
-
-Kinetikit 12 is a graphical interface for doing chemical kinetic
-modeling in MOOSE. It is derived in part from Kinetikit, which was the
-graphical interface used in GENESIS for similar models. Kinetikit, also
-known as kkit, was at version 11 with GENESIS. Here we start with
-Kinetikit 12.
-
-`**TODO** What are chemical kinetic models? <#TOC>`_
-----------------------------------------------------
-
-Much of neuronal computation occurs through chemical signaling. For
-example, many forms of synaptic plasticity begin with calcium influx
-into the synapse, followed by calcium binding to calmodulin, and then
-calmodulin activation of numerous enzymes. These events can be
-represented in chemical terms:
-
- 4 Ca2+ + CaM <===> Ca4.CaM
-
-Such chemical equations can be modeled through standard Ordinary
-Differential Equations, if we ignore space:
-
- d[Ca]/dt = −4Kf ∗ [Ca]4 ∗ [CaM] + 4Kb ∗ [Ca4.CaM] d[CaM]/dt = −Kf ∗
- [Ca]4 ∗ [CaM] + Kb ∗ [Ca4.CaM] d[Ca4.CaM]/dt = Kf ∗ [Ca]4 ∗ [CaM] −
- Kb ∗ [Ca4.CaM]
-
-MOOSE models these chemical systems. This help document describes how to
-do such modelling using the graphical interface, Kinetikit 12.
-
-`Levels of model <#TOC>`_
-~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Chemical kinetic models can be simple well-stirred (or point) models, or
-they could have multiple interacting compartments, or they could include
-space explicitly using reaction-diffusion. In addition such models could
-be solved either deterministically, or using a stochastic formulation.
-At present Kinetikit handles compartmental models but does not compute
-diffusion within the compartments, though MOOSE itself can do this at
-the script level. Kkit12 will do deterministic as well as stochastic
-chemical calculations.
-
-`Numerical methods <#TOC>`_
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-- **Deterministic**: Adaptive timestep 5th order Runge-Kutta-Fehlberg
- from the GSL (GNU Scientific Library).
-- **Stochastic**: Optimized Gillespie Stochastic Systems Algorithm,
- custom implementation.
-
-`Using Kinetikit 12 <#TOC>`_
-----------------------------
-
-`Overview <#TOC>`_
-~~~~~~~~~~~~~~~~~~
-
-- Load models using **``File -> Load model``**. A reaction schematic
- for the chemical system appears in the **``Editor view``** tab.
-- View parameters in **``Editor view``** tab by clicking on icons, and
- looking at entries in **``Properties``** table to the right.
-- Edit parameters by changing their values in the **``Properties``**
- table.
-- From Run View, Pools can be plotted by clicking on their icons and
- dragging the icons onto the plot Window. Presently only concentration
- is plottable.
-- Run models using **``Run``** button.
-- Select numerical method using options under **``Preferences``**
- button in simulation control.
-- Save plots using the icons at the bottom of the **``Plot Window``**.
-
-Most of these operations are detailed in other sections, and are shared
-with other aspects of the MOOSE simulation interface. Here we focus on
-the Kinetikit-specific items.
-
-`Model layout and icons <#TOC>`_
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-When you are in the **``Model View``** (``Editor``) tab you will see a collection of
-icons, arrows, and grey boxes surrounding these. This is a schematic of
-the reaction scheme being modeled. You can view and change parameters,
-and change the layout of the model.
-
-.. figure:: ../../images/Moose1.png
- :align: center
- :alt:
-
-Resizing the model layout and icons:
-
-- **Zoom**: Comma and period keys. Alternatively, the mouse scroll
- wheel or vertical scroll line on the track pad will cause the display
- to zoom in and out.
-- **Pan**: The arrow keys move the display left, right, up, and down.
-- **Entire Model View**: Pressing the **``a``** key will fit the entire
- model into the entire field of view.
-- **Resize Icons**: Angle bracket keys, that is, **``<``** and
- **``>``** or **``+``** and **``-``**. This resizes the icons while
- leaving their positions on the screen layout more or less the same.
-- **Original Model View**: Presing the **``A``** key (capital ``A``)
- will revert to the original model view including the original icon
- scaling.
-
-`Compartment <#TOC>`_
-^^^^^^^^^^^^^^^^^^^^^
-
-The *compartment* in moose is usually a contiguous domain in which a
-certain set of chemical reactions and molecular species occur. The
-definition is very closely related to that of a cell-biological
-compartment. Examples include the extracellular space, the cell
-membrane, the cytosol, and the nucleus. Compartments can be nested, but
-of course you cannot put a bigger compartment into a smaller one.
-
-- **Icon**: Grey boundary around a set of reactions.
-- **Moving Compartments**: Click and drag on the boundary.
-- **Resizing Compartment boundary**: Happens automatically when
- contents are repositioned, so that the boundary just contains
- contents.
-- **Compartment editable parameters**:
-
- - **``name``**: The name of the compartment.
- - **``size``**: This is the volume, surface area or length of the
- compartment, depending on its type.
-
-- **Compartment fixed parameters**:
-
- - **``numDimensions``**: This specifies whether the compartment is a
- volume, a 2-D surface, or if it is just being represented as a
- length.
-
-`Pool <#TOC>`_
-^^^^^^^^^^^^^^
-
-This is the set of molecules of a given species within a compartment.
-Different chemical states of the same molecule are in different pools.
-
-- **Icon**: |image0| Colored rectangle with pool name in it.
-- **Moving pools**: Click and drag.
-- **Pool editable parameters**:
-
- - **``name``**: Name of the pool
- - **``n``**: Number of molecules in the pool
- - **``nInit``**: Initial number of molecules in the pool. ``n`` gets
- set to this value when the ``reinit`` operation is done.
- - **``conc``**: Concentration of the molecules in the pool.
-
- conc = n \* unit\_scale\_factor / (NA \* vol)
-
- - **``concInit``**: Initial concentration of the molecules in the
- pool.
-
- concInit = nInit \* unit\_scale\_factor / (NA \* vol) ``conc``
- is set to this value when the ``reinit`` operation is done.
-
-- **Pool fixed parameters**
-
- - **``size``**: Derived from the compartment that holds the pool.
- Specifies volume, surface area or length of the holding
- compartment.
-
-`Buffered pools <#TOC>`_
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Some pools are set to a fixed ``n``, that is number of molecules, and
-therefore a fixed concentration, throughout a simulation. These are
-buffered pools.
-
-- **Icon**: |image1| Colored rectangle with pool name in it.
-- **Moving Buffered pools**: Click and drag.
-- **Buffered Pool editable parameters**
-
- - **``name``**: Name of the pool
- - **``nInit``**: Fixed number of molecules in the pool. ``n`` gets
- set to this value throughout the run.
- - **``concInit``**: Fixed concentration of the molecules in the
- pool.
-
- concInit = nInit \* unit\_scale\_factor / (NA \* vol) ``conc``
- is set to this value throughout the run.
-
-- **Pool fixed parameters**:
-
- - **``n``**: Number of molecules in the pool. Derived from
- ``nInit``.
- - **``conc``**: Concentration of molecules in the pool. Derived from
- ``concInit``.
- - **``size``**: Derived from the compartment that holds the pool.
- Specifies volume, surface area or length of the holding
- compartment.
-
-`Reaction <#TOC>`_
-^^^^^^^^^^^^^^^^^^
-
-These are conversion reactions between sets of pools. They are
-reversible, but you can set either of the rates to zero to get
-irreversibility. In the illustration below, **``D``** and **``A``** are
-substrates, and **``B``** is the product of the reaction. This is
-indicated by the direction of the green arrow.
-
-.. figure:: ../../images/KkitReaction.png
- :align: center
- :alt:
-
-- **Icon**: |image2| Reversible reaction arrow.
-- **Moving Reactions**: Click and drag.
-- **Reaction editable parameters**:
-
- - name : Name of reaction
- - K\ :sub:`f`\ : Forward rate of reaction, in
- ``concentration/time`` units. This is the normal way to express
- and manipulate the reaction rate.
- - k\ :sub:`f`\ : Forward rate of reaction, in ``number/time``
- units. This is used internally for computations, but is
- volume-dependent and should not be used to manipulate the reaction
- rate unless you really know what you are doing.
- - K\ :sub:`b`\ : Backward rate of reaction, in
- ``concentration/time`` units. This is the normal way to express
- and manipulate the reaction rate.
- - k\ :sub:`b`\ : Backward rate of reaction, in ``number/time``
- units. This is used internally for computations, but is
- volume-dependent and should not be used to manipulate the reaction
- rate unless you really know what you are doing.
-
-- **Reaction fixed parameters**:
-
- - **numProducts**: Number of product molecules.
- - **numSubstrates**: Number of substrates molecules.
-
-`Mass-action enzymes <#TOC>`_
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-These are enzymes that model the chemical equations
-
- E + S <===> E.S -> E + P
-
-Note that the second reaction is irreversible. Note also that
-mass-action enzymes include a pool to represent the **``E.S``**
-(enzyme-substrate) complex. In the example below, the enzyme pool is
-named **``MassActionEnz``**, the substrate is **``C``**, and the product
-is **``E``**. The direction of the enzyme reaction is indicated by the
-red arrows.
-
-.. figure:: ../../images/MassActionEnzReac.png
- :align: center
- :alt:
-
-- **Icon**: |image3| Colored ellipse atop a small square. The ellipse
- represents the enzyme. The small square represents **``E.S``**, the
- enzyme-substrate complex. The ellipse icon has the same color as the
- enzyme pool **``E``**. It is connected to the enzyme pool **``E``**
- with a straight line of the same color.
-
- The ellipse icon sits on a continuous, typically curved arrow in red,
- from the substrate to the product.
-
- A given enzyme pool can have any number of enzyme activities, since
- the same enzyme might catalyze many reactions.
-
-- **Moving Enzymes**: Click and drag on the ellipse.
-- **Enzyme editable parameters**
-
- - name : Name of enzyme.
- - K\ :sub:`m`\ : Michaelis-Menten value for enzyme, in
- ``concentration`` units.
- - k\ :sub:`cat`\ : Production rate of enzyme, in ``1/time`` units.
- Equal to k\ :sub:`3`\ , the rate of the second, irreversible
- reaction.
- - k\ :sub:`1`\ : Forward rate of the **E+S** reaction, in number
- and ``1/time`` units. This is what is used in the internal
- calculations.
- - k\ :sub:`2`\ : Backward rate of the **E+S** reaction, in
- ``1/time`` units. Used in internal calculations.
- - k\ :sub:`3`\ : Forward rate of the **E.S -> E + P** reaction, in
- ``1/time`` units. Equivalent to k\ :sub:`cat`\ . Used in internal
- calculations.
- - ratio: This is equal to k\ :sub:`2`\ /k\ :sub:`3`\ . Needed to
- define the internal rates in terms of K\ :sub:`m`\ and
- k\ :sub:`cat`\ . I usually use a value of 4.
-
-- **Enzyme-substrate-complex editable parameters**: These are identical
- to those of any other pool.
-
- - **name**: Name of the **``E.S``** complex. Defaults to
- **``<enzymeName>_cplx``**.
- - **n**: Number of molecules in the pool
- - **nInit**: Initial number of molecules in the complex. ``n`` gets
- set to this value when the ``reinit`` operation is done.
- - **conc**: Concentration of the molecules in the pool.
-
- conc = n \* unit\_scale\_factor / (NA \* vol)
-
- - **``concInit``**: Initial concentration of the molecules in the
- pool.
-
- concInit = nInit \* unit\_scale\_factor / (NA \* vol) ``conc``
- is set to this value when the ``reinit`` operation is done.
-
-- **Enzyme-substrate-complex fixed parameters**:
-
- - **size**: Derived from the compartment that holds the pool.
- Specifies volume, surface area or length of the holding
- compartment. Note that the Enzyme-substrate-complex is assumed to
- be in the same compartment as the enzyme molecule.
-
-`Michaelis-Menten Enzymes <#TOC>`_
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-These are enzymes that obey the Michaelis-Menten equation
-
- V = Vmax \* [S] / ( Km + [S] ) = kcat \* [Etot] \* [S] / ( Km + [S]
- )
-
-where
-
-- V\ :sub:`max`\ is the maximum rate of the enzyme
-- [Etot] is the total amount of the enzyme
-- K\ :sub:`m`\ is the Michaelis-Menten constant
-- S is the substrate.
-
-Nominally these enzymes model the same chemical equation as the
-mass-action enzyme:
-
- E + S <===> E.S -> E + P
-
-but they make the assumption that the **``E.S``** is in a
-quasi-steady-state with **``E``** and **``S``**, and they also ignore
-sequestration of the enzyme into the complex. So there is no
-representation of the **``E.S``** complex. In the example below, the
-enzyme pool is named **``MM_Enz``**, the substrate is **``E``**, and the
-product is **``F``**. The direction of the enzyme reaction is indicated
-by the red arrows.
-
-.. figure:: ../../images/MM_EnzReac.png
- :align: center
- :alt:
-
-- **Icon**: |image4| Colored ellipse. The ellipse represents the enzyme
- The ellipse icon has the same color as the enzyme **``MM_Enz``**. It
- is connected to the enzyme pool **``MM_Enz``** with a straight line
- of the same color. The ellipse icon sits on a continuous, typically
- curved arrow in red, from the substrate to the product. A given
- enzyme pool can have any number of enzyme activities, since the same
- enzyme might catalyze many reactions.
-- **Moving Enzymes**: Click and drag.
-- **Enzyme editable parameters**:
-
- - name: Name of enzyme.
- - K\ :sub:`m`\ : Michaelis-Menten value for enzyme, in
- ``concentration`` units.
- - k\ :sub:`cat`\ : Production rate of enzyme, in ``1/time`` units.
- Equal to k\ :sub:`3`\ , the rate of the second, irreversible
- reaction.
-
-`Function <#TOC>`_
-^^^^^^^^^^^^^^^^^^
-
-Function objects can be used to evaluate expressions with arbitrary
-number of variables and constants. We can assign expression of the form:
-
-f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP )
-
-where ci‘s are constants and xi‘s and yi‘s are variables.
-
-It can parse mathematical expression defining a function and evaluate it
-and/or its derivative for specified variable values. The variables can
-be input from other moose objects. In case of arbitrary variable names,
-the source message must have the variable name as the first argument.
-
-- **Icon**: Colored rectangle with pool name. This is **``Æ’``** in the
- example image below. The input pools **``A``** and **``B``** connect
- to the **Æ’** with blue arrows. The function ouput's to BuffPool
-
-`Model operations <#TOC>`_
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-- **Loading models**: **``File -> Load Model -> select from dialog``**.
- This operation makes the previously loaded model disable and loads
- newly selected models in **``Model View``**
-- **New**: **``File -> New -> Model name``**. This opens a empty widget
- for model building
-- **Saving models**: **``File -> Save Model -> select from dialog``**.
-- **Changing numerical methods**: **``Preference->Chemical tab``** item
- from Simulation Control. Currently supports:
-
- - Runge Kutta: This is the Runge-Kutta-Fehlberg implementation from
- the GNU Scientific Library (GSL). It is a fifth order variable
- timestep explicit method. Works well for most reaction systems
- except if they have very stiff reactions.
- - Gillespie: Optimized Gillespie stochastic systems algorithm,
- custom implementation. This uses variable timesteps internally.
- Note that it slows down with increasing numbers of molecules in
- each pool. It also slows down, but not so badly, if the number of
- reactions goes up.
- - Exponential Euler:This methods computes the solution of partial
- and ordinary differential equations.
-
-`Model building <#TOC>`_
-~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. figure:: ../../images/chemical_CS.png
- :align: center
- :alt:
-
-- The Edit Widget includes various menu options and model icons on the
- top.\* Use the mouse buttton to click and drag icons from toolbar to
- Edit Widget, two things will happen, icon will appear in the editor
- widget and a object editor will pop up with lots of parameters with
- respect to moose object. Rules:
-
- ::
-
- * Firstly Compartment has to be created.
- (At present only single compartment model is allowed)
-
- - Enzyme should be dropped on a pool as parent and function should
- be dropped on buffPool for output
-
- - Drag in pool's and reaction on to the editor widget, now one can
- set up a reaction.Click on mooseObject drag the mouse (a black dotted line for ExpectedConnection will appear)
- to any object for connection.
- E.g Pool to reaction and reaction to pool. Pool to function and function to Pool.
- Specific connection type gets specific colored arrow. E.g.
- Green color arrow for specifying connection between reactant and
- product for reaction. Second order reaction can also be done by
- repeating the connection over again
- - Each connection can be deleted and using rubberband selection each moose object can be deleted
- - When clicked on pool object 4 icons comes up
-
- |delete| : This deletes the object, its associated connection and if its enzyme's parent then enzyme and its associated connection is also deleted.
-
- |clone| : Clones the object
-
- |move| : Object can be moved around
-
- |plot| : Plot the object in plotWidget at Graph 1
-
- Note: Missing icon means the operation is not permitted
-
-.. figure:: ../../images/Chemical_run.png
- :align: center
- :alt:
-
-- From run widget, pools are draggable to plot window for plotting.
- (Currently **``conc``** is plotted as default field) Plots are
- color-coded as per in model.
-- Model can be run by clicking start button. One can stop button in
- mid-stream and start up again without affectiong the calculations.
- The reset button clears the simulation.
-
-.. |image0| image:: ../../images/Pool.png
-.. |image1| image:: ../../images/BufPool.png
-.. |image2| image:: ../../images/KkitReacIcon.png
-.. |image3| image:: ../../images/MassActionEnzIcon.png
-.. |image4| image:: ../../images/MM_EnzIcon.png
-.. |delete| image:: ../../images/delete.png
-.. |clone| image:: ../../images/clone.png
-.. |move| image:: ../../images/move.png
-.. |plot| image:: ../../images/plot.png
\ No newline at end of file
diff --git a/moose-core/Docs/user/GUI/Makefile b/moose-core/Docs/user/GUI/Makefile
deleted file mode 100644
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--- a/moose-core/Docs/user/GUI/Makefile
+++ /dev/null
@@ -1,153 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-PAPER =
-BUILDDIR = _build
-
-# Internal variables.
-PAPEROPT_a4 = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
-help:
- @echo "Please use \`make <target>' where <target> is one of"
- @echo " html to make standalone HTML files"
- @echo " dirhtml to make HTML files named index.html in directories"
- @echo " singlehtml to make a single large HTML file"
- @echo " pickle to make pickle files"
- @echo " json to make JSON files"
- @echo " htmlhelp to make HTML files and a HTML help project"
- @echo " qthelp to make HTML files and a qthelp project"
- @echo " devhelp to make HTML files and a Devhelp project"
- @echo " epub to make an epub"
- @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
- @echo " latexpdf to make LaTeX files and run them through pdflatex"
- @echo " text to make text files"
- @echo " man to make manual pages"
- @echo " texinfo to make Texinfo files"
- @echo " info to make Texinfo files and run them through makeinfo"
- @echo " gettext to make PO message catalogs"
- @echo " changes to make an overview of all changed/added/deprecated items"
- @echo " linkcheck to check all external links for integrity"
- @echo " doctest to run all doctests embedded in the documentation (if enabled)"
-
-clean:
- -rm -rf $(BUILDDIR)/*
-
-html:
- $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
- $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
- $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
- @echo
- @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
- $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
- @echo
- @echo "Build finished; now you can process the pickle files."
-
-json:
- $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
- @echo
- @echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
- $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
- @echo
- @echo "Build finished; now you can run HTML Help Workshop with the" \
- ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
- $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
- @echo
- @echo "Build finished; now you can run "qcollectiongenerator" with the" \
- ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
- @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/MOOSE.qhcp"
- @echo "To view the help file:"
- @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/MOOSE.qhc"
-
-devhelp:
- $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
- @echo
- @echo "Build finished."
- @echo "To view the help file:"
- @echo "# mkdir -p $$HOME/.local/share/devhelp/MOOSE"
- @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/MOOSE"
- @echo "# devhelp"
-
-epub:
- $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
- @echo
- @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-latex:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo
- @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
- @echo "Run \`make' in that directory to run these through (pdf)latex" \
- "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo "Running LaTeX files through pdflatex..."
- $(MAKE) -C $(BUILDDIR)/latex all-pdf
- @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text:
- $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
- @echo
- @echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man:
- $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
- @echo
- @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo
- @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
- @echo "Run \`make' in that directory to run these through makeinfo" \
- "(use \`make info' here to do that automatically)."
-
-info:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo "Running Texinfo files through makeinfo..."
- make -C $(BUILDDIR)/texinfo info
- @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext:
- $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
- @echo
- @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes:
- $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
- @echo
- @echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck:
- $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
- @echo
- @echo "Link check complete; look for any errors in the above output " \
- "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest:
- $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
- @echo "Testing of doctests in the sources finished, look at the " \
- "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/moose-core/Docs/user/GUI/MooseGuiDocs.rst b/moose-core/Docs/user/GUI/MooseGuiDocs.rst
deleted file mode 100644
index d093bc49a03179eff08c5d01e16c2684af5bf164..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/GUI/MooseGuiDocs.rst
+++ /dev/null
@@ -1,256 +0,0 @@
---------------
-
-**MOOSE GUI: Graphical interface for MOOSE**
-============================================
-
-Upinder Bhalla, Harsha Rani, Aviral Goel
-
-Aug 28 2013.
-
---------------
-
-Contents
---------
-
-- `Introduction <#introduction>`_
-- `Interface <#interface>`_
-
- - `Menu Bar <#menu-bar>`_
-
- - `File <#menu-file>`_
-
- - `New <#file-new>`_
- - `Load Model <#file-load-model>`_
- - `Connect BioModels <#file-connect-biomodels>`_
- - `Quit <#file-quit>`_
-
- - `View <#menu-view>`_
-
- - `Editor View <#editor-view>`_
- - `Run View <#run-view>`_
- - `Dock Widgets <#dock-widgets>`_
- - `SubWindows <#subwindows>`_
-
- - `Help <#menu-help>`_
-
- - `About MOOSE <#about-moose>`_
- - `Built-in Documentation <#built-in-documentation>`_
- - `Report a bug <#report-a-bug>`_
-
- - `Editor View <#editor-view>`_
-
- - `Model Editor <#model-editor>`_
- - `Property Editor <#property-editor>`_
-
- - `Run View <#run-view>`_
-
- - `Simulation Controls <#simulation-controls>`_
- - `Plot Widget <#plot-widget>`_
-
- - `Toolbar <#plot-widget-toolbar>`_
- - `Context Menu <#plot-widget-context-menu>`_
-
-Introduction
-------------
-
-The Moose GUI currently allow you work on
-`chemical <Kkit12Documentation.html>`_ models using a interface. This
-document describes the salient features of the GUI
-
-Interface
----------
-
-The interface layout consists of a `menu bar <#menu-bar>`_ and two
-views, `editor view <#editor-view>`_ and `run view <#run-view>`_.
-
-Menu Bar
-~~~~~~~~
-
-.. figure:: ../../images/MooseGuiMenuImage.png
- :align: center
- :alt:
-
-The menu bar appears at the top of the main window. In Ubuntu 12.04, the
-menu bar appears only when the mouse is in the top menu strip of the
-screen. It consists of the following options -
-
-File
-^^^^
-
-The File menu option provides the following sub options -
-
-- `New <#file-new>`_ - Create a new chemical signalling model.
-- `Load Model <#file-load-model>`_ - Load a chemical signalling or
- compartmental neuronal model from a file.
-- `Paper\_2015\_Demos Model <#paper-2015-demos-model>`_ - Loads and
- Runs chemical signalling or compartmental neuronal model from a file.
-- `Recently Loaded Models <#recently-loaded-models>`_ - List of models
- loaded in MOOSE. (Atleast one model should be loaded)
-- `Connect BioModels <#file-connect-biomodels>`_ - Load chemical
- signaling models from the BioModels database.
-- `Save <#file-quit>`_ - Saves chemical model to Genesis/SBML format.
-- `Quit <#file-quit>`_ - Quit the interface.
-
-View
-^^^^
-
-View menu option provides the following sub options -
-
-- `Editor View <#editor-view>`_ - Switch to the editor view for editing
- models.
-- `Run View <#run-view>`_ - Switch to run view for running models.
-- `Dock Widgets <#dock-widgets>`_ - Following dock widgets are provided
- -
-
- - `Python <#dock-widget-python>`_ - Brings up a full fledged python
- interpreter integrated with MOOSE GUI. You can interact with
- loaded models and load new models through the PyMoose API. The
- entire power of python language is accessible, as well as
- MOOSE-specific functions and classes.
- - `Edit <#dock-widget-edit>`_ - A property editor for viewing and
- editing the fields of a selected object such as a pool, enzyme,
- function or compartment. Editable field values can be changed by
- clicking on them and overwriting the new values. Please be sure to
- press enter once the editing is complete, in order to save your
- changes.
-
-- `SubWindows <#subwindows>`_ - This allows you to tile or tabify the
- run and editor views.
-
-Help
-^^^^
-
-- `About Moose <#about-moose>`_ - Version and general information about
- MOOSE.
-- `Built-in documentation <#butilt-in-documentation>`_ - Documentation
- of MOOSE GUI.
-- `Report a bug <#report-a-bug>`_ - Directs to the github bug tracker
- for reporting bugs.
-
-Editor View
-~~~~~~~~~~~
-
-The editor view provides two windows -
-
-- `Model Editor <#model-editor>`_ - The model editor is a workspace to
- edit and create models. Using click-and-drag from the icons in the
- menu bar, you can create model entities such as chemical pools,
- reactions, and so on. A click on any object brings its property
- editor on screen (see below). In objects that can be interconnected,
- a click also brings up a special arrow icon that is used to connect
- objects together with messages. You can move objects around within
- the edit window using click-and-drag. Finally, you can delete objects
- by selecting one or more, and then choosing the delete option from
- the pop-up menu. The links below is the screenshots point to the
- details for the chemical signalling model editor.
-
-.. figure:: ../../images/ChemicalSignallingEditor.png
- :align: center
- :alt: Chemical Signalling Model Editor
-
- Chemical Signalling Model Editor
-
-- `Property Editor <#property-editor>`_ - The property editor provides
- a way of viewing and editing the properties of objects selected in
- the model editor.
-
-.. figure:: ../../images/PropertyEditor.png
- :align: center
- :alt: Property Editor
-
- Property Editor
-Run View
-~~~~~~~~
-
-The Run view, as the name suggests, puts the GUI into a mode where the
-model can be simulated. As a first step in this, you can click-and-drag
-an object to the graph window in order to create a time-series plot for
-that object. For example, in a chemical reaction, you could drag a pool
-into the graph window and subsequent simulations will display a graph of
-the concentration of the pool as a function of time. Within the Run View
-window, the time-evolution of the simulation is displayed as an
-animation. For chemical kinetic models, the size of the icons for
-reactant pools scale to indicate concentration. Above the Run View
-window, there is a special tool bar with a set of simulation controls to
-run the simulation.
-
-Simulation Controls
-^^^^^^^^^^^^^^^^^^^
-
-.. figure:: ../../images/SimulationControl.png
- :align: center
- :alt: Simulation Control
-
- Simulation Control
-This panel allows you to control the various aspects of the simulation.
-
-- `Run Time <#run-time>`_ - Determines duration for which simulation is
- to run. A simulation which has already run, runs further for the
- specified additional period.
-- `Reset <#reset>`_ - Restores simulation to its initial state;
- re-initializes all variables to t = 0.
-- `Stop <#stop>`_ - This button halts an ongoing simulation.
-- `Current time <#current-time>`_ - This reports the current simulation
- time.
-- `Preferences <#preferences>`_ - Allows you to set simulation and
- visualization related preferences.
-
-Plot Widget
-^^^^^^^^^^^
-
-Toolbar
-'''''''
-
-On top of plot window there is a little row of icons:
-
-.. figure:: ../../images/PlotWindowIcons.png
- :align: center
- :alt:
-
-These are the plot controls. If you hover the mouse over them for a few
-seconds, a tooltip pops up. The icons represent the following functions:
-
-- |image0| - Add a new plot window
-
-- |image1| - Deletes current plot window
-
-- |image2| - Toggle X-Y axis grid
-
-- |image3| - Returns the plot display to its default position
-
-- |image4| - Undoes or re-does manipulations you have done to the
- display.
-
-- |image5| - The plots will pan around with the mouse when you hold the
- left button down. The plots will zoom with the mouse when you hold
- the right button down.
-
-- |image6| - With the **``left mouse button``**, this will zoom in to
- the specified rectangle so that the plots become bigger. With the
- **``right mouse button``**, the entire plot display will be shrunk to
- fit into the specified rectangle.
-
-- |image7| - You don't want to mess with these .
-
-- |image8| - Save the plot.
-
-Context Menu
-''''''''''''
-
-The context menu is enabled by right clicking on the plot window. It has
-the following options -
-
-- **Export to CSV** - Exports the plotted data to CSV format
-- **Toggle Legend** - Toggles the plot legend
-- **Remove** - Provides a list of plotted entities. The selected entity
- will not be plotted.
-
-.. |image0| image:: ../../images/Addgraph.png
-.. |image1| image:: ../../images/delgraph.png
-.. |image2| image:: ../../images/grid.png
-.. |image3| image:: ../../images/MatPlotLibHomeIcon.png
-.. |image4| image:: ../../images/MatPlotLibDoUndo.png
-.. |image5| image:: ../../images/MatPlotLibPan.png
-.. |image6| image:: ../../images/MatPlotLibZoom.png
-.. |image7| image:: ../../images/MatPlotLibConfigureSubplots.png
-.. |image8| image:: ../../images/MatPlotLibSave.png
diff --git a/moose-core/Docs/user/GUI/RdesigneurDocumentation.rst b/moose-core/Docs/user/GUI/RdesigneurDocumentation.rst
deleted file mode 100644
index 59550378c91c1f242b4eacccf0b3a0f2c3c4db62..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/GUI/RdesigneurDocumentation.rst
+++ /dev/null
@@ -1,801 +0,0 @@
---------------
-
-**Rdesigneur: Building multiscale models**
-==========================================
-
-Upi Bhalla
-
-Dec 28 2015.
-
---------------
-
-Contents
---------
-
-Introduction
-------------
-
-**Rdesigneur** (Reaction Diffusion and Electrical SIGnaling in NEURons)
-is an interface to the multiscale modeling capabilities in MOOSE. It is
-designed to build models incorporating biochemical signaling pathways in
-dendrites and spines, coupled to electrical events in neurons.
-Rdesigneur assembles models from predefined parts: it delegates the
-details to specialized model definition formats. Rdesigneur combines one
-or more of the following cell parts to build models:
-
-- Neuronal morphology
-- Dendritic spines
-- Ion channels
-- Reaction systems
-
-Rdesigneur's main role is to specify how these are put together,
-including assigning parameters to do so. Rdesigneur also helps with
-setting up the simulation input and output.
-
-Quick Start
------------
-
-Here we provide a few use cases, building up from a minimal model to a
-reasonably complete multiscale model spanning chemical and electrical
-signaling.
-
-Bare Rdesigneur: single passive compartment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-If we don't provide any arguments at all to the Rdesigneur, it makes a
-model with a single passive electrical compartment in the MOOSE path
-``/model/elec/soma``. Here is how to do this:
-
-::
-
- import moose
- import rdesigneur as rd
- rdes = rd.rdesigneur()
- rdes.buildModel()
-
-To confirm that it has made a compartment with some default values we
-can add a line:
-
-::
-
- moose.showfields( rdes.soma )
-
-This should produce the output:
-
-::
-
- [ /model[0]/elec[0]/soma[0] ]
- diameter = 0.0005
- fieldIndex = 0
- Ra = 7639437.26841
- y0 = 0.0
- Rm = 424413.177334
- index = 0
- numData = 1
- inject = 0.0
- initVm = -0.065
- Em = -0.0544
- y = 0.0
- numField = 1
- path = /model[0]/elec[0]/soma[0]
- dt = 0.0
- tick = -2
- z0 = 0.0
- name = soma
- Cm = 7.85398163398e-09
- x0 = 0.0
- Vm = -0.06
- className = ZombieCompartment
- idValue = 465
- length = 0.0005
- Im = 1.3194689277e-08
- x = 0.0005
- z = 0.0
-
-Simulate and display current pulse to soma
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-A more useful script would run and display the model. Rdesigneur can
-help with the stimulus and the plotting. This simulation has the same
-passive compartment, and current is injected as the simulation runs.
-This script displays the membrane potential of the soma as it charges
-and discharges.
-
-::
-
- import moose
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- stimList = [['soma', '1', 'inject', '(t>0.1 && t<0.2) * 2e-8']],
- plotList = [['soma', '1', 'Vm', 'Soma membrane potential']],
- )
- rdes.buildModel()
- moose.reinit()
- moose.start( 0.3 )
- rdes.display()
-
-The *stimList* defines a stimulus. Each entry has four arguments:
-
-::
-
- `[region_in_cell, region_expression, parameter, expression_string]`
-
-- ``region_in_cell`` specifies the objects to stimulate. Here it is
- just the soma.
-- ``region_expression`` specifies a geometry based calculation to
- decide whether to apply the stimulus. The value must be >0 for the
- stimulus to be present. Here it is just 1.
-- ``parameter`` specifies the simulation parameter to assign. Here it
- is the injection current to the compartment.
-- ``expression_string`` calculates the value of the parameter,
- typically as a function of time. Here we use the function sign(x),
- where sign(x) == +1 for x > 0, 0 for x = 0 and -1 for x < 0.
-
-To summarise this, the *stimList* here means *inject a current of 20nA
-to the soma between the times of 0.1 and 0.2 s*.
-
-The *plotList* defines what to plot. It has a similar set of arguments:
-
-::
-
- `[region_in_cell, region_expression, parameter, title_of_plot]`
-
-These mean the same thing as for the stimList except for the title of
-the plot.
-
-The *rdes.display()* function causes the plots to be displayed.
-
-.. figure:: ../../images/rdes2_passive_squid.png
- :align: center
- :alt: Plot for current input to passive compartment
-
- Plot for current input to passive compartment
-When we run this we see an initial depolarization as the soma settles
-from its initial -65 mV to a resting Em = -54.4 mV. These are the
-original HH values, see the example above. At t = 0.1 seconds there is
-another depolarization due to the current injection, and at t = 0.2
-seconds this goes back to the resting potential.
-
-HH Squid model in a single compartment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Here we put the Hodgkin-Huxley squid model channels into a passive
-compartment. The HH channels are predefined as prototype channels for
-Rdesigneur,
-
-::
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- chanProto = [['make_HH_Na()', 'Na'], ['make_HH_K()', 'K']],
- chanDistrib = [
- ['Na', 'soma', 'Gbar', '1200' ],
- ['K', 'soma', 'Gbar', '360' ]],
- stimList = [['soma', '1', 'inject', '(t>0.1 && t<0.2) * 1e-8' ]],
- plotList = [['soma', '1', 'Vm', 'Membrane potential']]
- )
-
- rdes.buildModel()
- moose.reinit()
- moose.start( 0.3 )
- rdes.display()
-
-Here we introduce two new model specification lines:
-
-- **chanProto**: This specifies which ion channels will be used in the
- model. Each entry here has two fields: the source of the channel
- definition, and (optionally) the name of the channel. In this example
- we specify two channels, an Na and a K channel using the original
- Hodgkin-Huxley parameters. As the source of the channel definition we
- use the name of the Python function that builds the channel. The
- *make\_HH\_Na()* and *make\_HH\_K()* functions are predefined but we
- can also specify our own functions for making prototypes. We could
- also have specified the channel prototype using the name of a channel
- definition file in ChannelML (a subset of NeuroML) format.
-- **chanDistrib**: This specifies *where* the channels should be placed
- over the geometry of the cell. Each entry in the chanDistrib list
- specifies the distribution of parameters for one channel using four
- entries:
-
- ``[object_name, region_in_cell, parameter, expression_string]``
-
- In this case the job is almost trivial, since we just have a single
- compartment named *soma*. So the line
-
- ``['Na', 'soma', 'Gbar', '1200' ]``
-
- means *Put the Na channel in the soma, and set its maximal
- conductance density (Gbar) to 1200 Siemens/m^2*.
-
-As before we apply a somatic current pulse. Since we now have HH
-channels in the model, this generates action potentials.
-
-.. figure:: ../../images/rdes3_squid.png
- :align: center
- :alt: Plot for HH squid simulation
-
- Plot for HH squid simulation
-Reaction system in a single compartment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Here we use the compartment as a place in which to embed a chemical
-model. The chemical oscillator model is predefined in the rdesigneur
-prototypes.
-
-::
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- turnOffElec = True,
- diffusionLength = 1e-3, # Default diffusion length is 2 microns
- chemProto = [['make_Chem_Oscillator()', 'osc']],
- chemDistrib = [['osc', 'soma', 'install', '1' ]],
- plotList = [['soma', '1', 'dend/a', 'conc', 'a Conc'],
- ['soma', '1', 'dend/b', 'conc', 'b Conc']]
- )
- rdes.buildModel()
- b = moose.element( '/model/chem/dend/b' )
- b.concInit *= 5
- moose.reinit()
- moose.start( 200 )
-
- rdes.display()
-
-In this special case we set the turnOffElec flag to True, so that
-Rdesigneur only sets up chemical and not electrical calculations. This
-makes the calculations much faster, since we disable electrical
-calculations and delink chemical calculations from them.
-
-We also have a line which sets the ``diffusionLength`` to 1 mm, so that
-it is bigger than the 0.5 mm squid axon segment in the default
-compartment. If you don't do this the system will subdivide the
-compartment into 2 micron voxels for the purposes of putting in a
-reaction-diffusion system, which we discuss below.
-
-There are a couple of lines to change the initial concentration of the
-molecular pool b. It is scaled up 5x to give rise to slowly decaying
-oscillations.
-
-.. figure:: ../../images/rdes4_osc.png
- :align: center
- :alt: Plot for single-compartment reaction simulation
-
- Plot for single-compartment reaction simulation
-Reaction-diffusion system
-~~~~~~~~~~~~~~~~~~~~~~~~~
-
-In order to see what a reaction-diffusion system looks like, delete the
-``diffusionLength`` expression in the previous example and add a couple
-of lines to set up 3-D graphics for the reaction-diffusion product:
-
-::
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- turnOffElec = True,
- chemProto = [['make_Chem_Oscillator()', 'osc']],
- chemDistrib = [['osc', 'soma', 'install', '1' ]],
- plotList = [['soma', '1', 'dend/a', 'conc', 'Concentration of a'],
- ['soma', '1', 'dend/b', 'conc', 'Concentration of b']],
- moogList = [['soma', '1', 'dend/a', 'conc', 'a Conc', 0, 360 ]]
- )
-
- rdes.buildModel()
- bv = moose.vec( '/model/chem/dend/b' )
- bv[0].concInit *= 2
- bv[-1].concInit *= 2
- moose.reinit()
-
- rdes.displayMoogli( 1, 400, 0.001 )
-
-This is the line we deleted.
-
-::
-
- `diffusionLength = 1e-3,`
-
-With this change we permit *rdesigneur* to use the default diffusion
-length of 2 microns. The 500-micron axon segment is now subdivided into
-250 voxels, each of which has a reaction system and diffusing molecules.
-To make it more picturesque, we have added a line after the plotList, to
-display the outcome in 3-D:
-
-::
-
- 'moogList = [['soma', '1', 'dend/a', 'conc', 'a Conc', 0, 360 ]]'
-
-This line says: take the model compartments defined by ``soma`` as the
-region to display, do so throughout the the geometry (the ``1``
-signifies this), and over this range find the chemical entity defined by
-``dend/a``. For each ``a`` molecule, find the ``conc`` and dsiplay it.
-There are two optional arguments, ``0`` and ``360``, which specify the
-low and high value of the displayed variable.
-
-In order to initially break the symmetry of the system, we change the
-initial concentration of molecule b at each end of the cylinder:
-
-::
-
- bv[0].concInit *= 2
- bv[-1].concInit *= 2
-
-If we didn't do this the entire system would go through a few cycles of
-decaying oscillation and then reach a boring, spatially uniform, steady
-state. Try putting an initial symmetry break elsewhere to see what
-happens.
-
-To display the concenctration changes in the 3-D soma as the simulation
-runs, we use the line
-
-::
-
- `rdes.displayMoogli( 1, 400, 0.001 )`
-
-The arguments mean: *displayMoogli( frametime, runtime, rotation )*
-Here,
-
-::
-
- frametime = time by which simulation advances between display updates
- runtime = Total simulated time
- rotation = angle by which display rotates in each frame, in radians.
-
-When we run this, we first get a 3-D display with the oscillating
-reaction-diffusion system making its way inward from the two ends. After
-the simulation ends the plots for all compartments for the whole run
-come up.
-
-.. figure:: ../../images/rdes5_reacdiff.png
- :align: center
- :alt: Display for oscillatory reaction-diffusion simulation
-
- Display for oscillatory reaction-diffusion simulation
-Primer on using the 3-D MOOGLI display
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Here is a short primer on the 3-D display controls.
-
-- *Roll, pitch, and yaw*: Use the letters *r*, *p*, and *y*. To rotate
- backwards, use capitals.
-- *Zoom out and in*: Use the *,* and *.* keys, or their upper-case
- equivalents, *<* and *>*. Easier to remember if you think in terms of
- the upper-case.
-- *Left/right/up/down*: Arrow keys.
-- *Quit*: control-q or control-w.
-- You can also use the mouse or trackpad to control most of the above.
-- By default rdesigneur gives Moogli a small rotation each frame. It is
- the *rotation* argument in the line:
-
- ``displayMoogli( frametime, runtime, rotation )``
-
-These controls operate over and above this rotation, but the rotation
-continues. If you set the rotation to zero you can, with a suitable
-flick of the mouse, get the image to rotate in any direction you choose
-as long as the window is updating.
-
-Make a toy multiscale model with electrical and chemical signaling.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Now we put together chemical and electrical models. In this toy model we
-have an HH-squid type single compartment electrical model, cohabiting
-with a chemical oscillator. The chemical oscillator regulates K+ channel
-amounts, and the average membrane potential regulates the amounts of a
-reactant in the chemical oscillator. This is a recipe for some strange
-firing patterns.
-
-::
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- # We want just one compartment so we set diffusion length to be
- # bigger than the 0.5 mm HH axon compartment default.
- diffusionLength = 1e-3,
- chanProto = [['make_HH_Na()', 'Na'], ['make_HH_K()', 'K']],
- chanDistrib = [
- ['Na', 'soma', 'Gbar', '1200' ],
- ['K', 'soma', 'Gbar', '360' ]],
- chemProto = [['make_Chem_Oscillator()', 'osc']],
- chemDistrib = [['osc', 'soma', 'install', '1' ]],
- # These adaptor parameters give interesting-looking but
- # not particularly physiological behaviour.
- adaptorList = [
- [ 'dend/a', 'conc', 'Na', 'modulation', 1, -5.0 ],
- [ 'dend/b', 'conc', 'K', 'modulation', 1, -0.2],
- [ 'dend/b', 'conc', '.', 'inject', -1.0e-7, 4e-7 ],
- [ '.', 'Vm', 'dend/s', 'conc', 2.5, 20.0 ]
- ],
- plotList = [['soma', '1', 'dend/a', 'conc', 'a Conc'],
- ['soma', '1', 'dend/b', 'conc', 'b Conc'],
- ['soma', '1', 'dend/s', 'conc', 's Conc'],
- ['soma', '1', 'Na', 'Gk', 'Na Gk'],
- ['soma', '1', '.', 'Vm', 'Membrane potential']
- ]
- )
-
- rdes.buildModel()
- moose.reinit()
- moose.start( 250 ) # Takes a few seconds to run this.
-
- rdes.display()
-
-We've already modeled the HH squid model and the oscillator
-individually, and you should recognize the parts of those models above.
-The new section that makes this work the *adaptorList* which specifies
-how the electrical and chemical parts talk to each other. This entirely
-fictional set of interactions goes like this:
-
-::
-
- [ 'dend/a', 'conc', 'Na', 'modulation', 1, -5.0 ]
-
-- *dend/a*: The originating variable comes from the 'a' pool on the
- 'dend' compartment.
-
- *conc*: This is the originating variable name on the 'a' pool.
-
- *Na*: This is the target variable
-
- *modulation*: scale the Gbar of Na up and down. Use 'modulation'
- rather than direct assignment of Gbar since Gbar is different for
- each differently-sized compartment.
-
- *1*: This is the initial offset
-
- *-5.0*: This is the scaling from the input to the parameter updated
- in the simulation.
-
-A similar set of adaptor entries couple the molecule *dend/b* to the K
-channel, *dend/b* again to the current injection into the soma, and the
-membrane potential to the concentration of *dend/s*.
-
-.. figure:: ../../images/rdes6_multiscale.png
- :align: center
- :alt: Plot for toy multiscale model
-
- Plot for toy multiscale model
-Morphology: Load .swc morphology file and view it
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Here we build a passive model using a morphology file in the .swc file
-format (as used by NeuroMorpho.org). The morphology file is predefined
-for Rdesigneur and resides in the directory ``./cells``. We apply a
-somatic current pulse, and view the somatic membrane potential in a
-plot, as before. To make things interesting we display the morphology in
-3-D upon which we represent the membrane potential as colors.
-
-::
-
- import moose
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- cellProto = [['./cells/h10.CNG.swc', 'elec']],
- stimList = [['soma', '1', '.', 'inject', 't * 25e-9' ]],
- plotList = [['#', '1', '.', 'Vm', 'Membrane potential'],
- ['#', '1', 'Ca_conc', 'Ca', 'Ca conc (uM)']],
- moogList = [['#', '1', '.', 'Vm', 'Soma potential']]
- )
-
- rdes.buildModel()
-
- moose.reinit()
- rdes.displayMoogli( 0.0002, 0.1 )
-
-Here the new concept is the cellProto line, which loads in the specified
-cell model:
-
-::
-
- `[ filename, cellname ]`
-
-The system recognizes the filename extension and builds a model from the
-swc file. It uses the cellname **elec** in this example.
-
-We use a similar line as in the reaction-diffusion example, to build up
-a Moogli display of the cell model:
-
-::
-
- `moogList = [['#', '1', '.', 'Vm', 'Soma potential']]`
-
-Here we have:
-
-::
-
- *#*: the path to use for selecting the compartments to display.
- This wildcard means use all compartments.
- *1*: The expression to use for the compartments. Again, `1` means use
- all of them.
- *.*: Which object in the compartment to display. Here we are using the
- compartment itself, so it is just a dot.
- *Vm*: Field to display
- *Soma potential*: Title for display.
-
-.. figure:: ../../images/rdes7_passive.png
- :align: center
- :alt: 3-D display for passive neuron
-
- 3-D display for passive neuron
-Build an active neuron model by putting channels into a morphology file
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-We load in a morphology file and distribute voltage-gated ion channels
-over the neuron. Here the voltage-gated channels are obtained from a
-number of channelML files, located in the ``./channels`` subdirectory.
-Since we have a spatially extended neuron, we need to specify the
-spatial distribution of channel densities too.
-
-::
-
- import moose
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- chanProto = [
- ['./chans/hd.xml'],
- ['./chans/kap.xml'],
- ['./chans/kad.xml'],
- ['./chans/kdr.xml'],
- ['./chans/na3.xml'],
- ['./chans/nax.xml'],
- ['./chans/CaConc.xml'],
- ['./chans/Ca.xml']
- ],
- cellProto = [['./cells/h10.CNG.swc', 'elec']],
- chanDistrib = [ \
- ["hd", "#dend#,#apical#", "Gbar", "50e-2*(1+(p*3e4))" ],
- ["kdr", "#", "Gbar", "p < 50e-6 ? 500 : 100" ],
- ["na3", "#soma#,#dend#,#apical#", "Gbar", "850" ],
- ["nax", "#soma#,#axon#", "Gbar", "1250" ],
- ["kap", "#axon#,#soma#", "Gbar", "300" ],
- ["kap", "#dend#,#apical#", "Gbar",
- "300*(H(100-p*1e6)) * (1+(p*1e4))" ],
- ["Ca_conc", "#", "tau", "0.0133" ],
- ["kad", "#soma#,#dend#,#apical#", "Gbar", "50" ],
- ["Ca", "#", "Gbar", "50" ]
- ],
- stimList = [['soma', '1', '.', 'inject', '(t>0.02) * 1e-9' ]],
- plotList = [['#', '1', '.', 'Vm', 'Membrane potential'],
- ['#', '1', 'Ca_conc', 'Ca', 'Ca conc (uM)']],
- moogList = [['#', '1', 'Ca_conc', 'Ca', 'Calcium conc (uM)', 0, 120],
- ['#', '1', '.', 'Vm', 'Soma potential']]
- )
-
- rdes.buildModel()
-
- moose.reinit()
- rdes.displayMoogli( 0.0002, 0.052 )
-
-Here we make more extensive use of two concepts which we've already seen
-from the single compartment squid model:
-
-1. *chanProto*: This defines numerous channels, each of which is of the
- form:
-
- ``[ filename ]``
-
- or
-
- ``[ filename, channelname ]``
-
-If the *channelname* is not specified the system uses the last part of
-the channel name, before the filetype suffix.
-
-2. *chanDistrib*: This defines the spatial distribution of each channel
- type. Each line is of a form that should be familiar now:
-
- ``[channelname, region_in_cell, parameter, expression_string]``
-
-- The *channelname* is the name of the prototype from *chanproto*. This
- is usually an ion channel, but in the example above you can also see
- a calcium concentration pool defined.
-- The *region\_in\_cell* is typically defined using wildcards, so that
- it generalizes to any cell morphology. For example, the plain
- wildcard ``#`` means to consider all cell compartments. The wildcard
- ``#dend#`` means to consider all compartments with the string
- ``dend`` somewhere in the name. Wildcards can be comma-separated, so
- ``#soma#,#dend#`` means consider all compartments with either soma or
- dend in their name. The naming in MOOSE is defined by the model file.
- Importantly, in **.swc** files MOOSE generates names that respect the
- classification of compartments into axon, soma, dendrite, and apical
- dendrite compartments respectively. SWC files generate compartment
- names such as:
-
- ::
-
- soma_<number>
- dend_<number>
- apical_<number>
- axon_<number>
-
-where the number is automatically assigned by the reader. In order to
-select all dendritic compartments, for example, one would use *"#dend#"*
-where the *"#"* acts as a wildcard to accept any string. - The
-*parameter* is usually Gbar, the channel conductance density in *S/m^2*.
-If *Gbar* is zero or less, then the system economizes by not
-incorporating this channel mechanism in this part of the cell.
-Similarly, for calcium pools, if the *tau* is below zero then the
-calcium pool object is simply not inserted into this part of the cell. -
-The *expression\_string* defines the value of the parameter, such as
-Gbar. This is typically a function of position in the cell. The
-expression evaluator knows about several parameters of cell geometry.
-All units are in metres:
-
-- *x*, *y* and *z* coordinates.
-- *g*, the geometrical distance from the soma
-- *p*, the path length from the soma, measured along the dendrites.
-- *dia*, the diameter of the dendrite.
-- *L*, The electrotonic length from the soma (no units).
-
-Along with these geometrical arguments, we make liberal use of the
-Heaviside function H(x) to set up the channel distributions. The
-expression evaluator also knows about pretty much all common algebraic,
-trignometric, and logarithmic functions, should you wish to use these.
-
-Also note the two Moogli displays. The first is the calcium
-concentration. The second is the membrane potential in each compartment.
-Easy!
-
-.. figure:: ../../images/rdes8_active.png
- :align: center
- :alt: 3-D display for active neuron
-
- 3-D display for active neuron
-Build a spiny neuron from a morphology file and put active channels in it.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This model is one step elaborated from the previous one, in that we now
-also have dendritic spines. MOOSE lets one decorate a bare neuronal
-morphology file with dendritic spines, specifying various geometric
-parameters of their location. As before, we use an swc file for the
-morphology, and the same ion channels and distribution.
-
-::
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- chanProto = [
- ['./chans/hd.xml'],
- ['./chans/kap.xml'],
- ['./chans/kad.xml'],
- ['./chans/kdr.xml'],
- ['./chans/na3.xml'],
- ['./chans/nax.xml'],
- ['./chans/CaConc.xml'],
- ['./chans/Ca.xml']
- ],
- cellProto = [['./cells/h10.CNG.swc', 'elec']],
- spineProto = [['make_active_spine()', 'spine']],
- chanDistrib = [
- ["hd", "#dend#,#apical#", "Gbar", "50e-2*(1+(p*3e4))" ],
- ["kdr", "#", "Gbar", "p < 50e-6 ? 500 : 100" ],
- ["na3", "#soma#,#dend#,#apical#", "Gbar", "850" ],
- ["nax", "#soma#,#axon#", "Gbar", "1250" ],
- ["kap", "#axon#,#soma#", "Gbar", "300" ],
- ["kap", "#dend#,#apical#", "Gbar",
- "300*(H(100-p*1e6)) * (1+(p*1e4))" ],
- ["Ca_conc", "#", "tau", "0.0133" ],
- ["kad", "#soma#,#dend#,#apical#", "Gbar", "50" ],
- ["Ca", "#", "Gbar", "50" ]
- ],
- spineDistrib = [['spine', '#dend#,#apical#', '20e-6', '1e-6']],
- stimList = [['soma', '1', '.', 'inject', '(t>0.02) * 1e-9' ]],
- plotList = [['#', '1', '.', 'Vm', 'Membrane potential'],
- ['#', '1', 'Ca_conc', 'Ca', 'Ca conc (uM)']],
- moogList = [['#', '1', 'Ca_conc', 'Ca', 'Calcium conc (uM)', 0, 120],
- ['#', '1', '.', 'Vm', 'Soma potential']]
- )
-
- rdes.buildModel()
-
- moose.reinit()
- rdes.displayMoogli( 0.0002, 0.023 )
-
-Spines are set up in a familiar way: we first define one (or more)
-prototype spines, and then distribute these around the cell. Here is the
-prototype string:
-
-::
-
- [spine_proto, spinename]
-
-*spine\_proto*: This is typically a function. One can define one's own,
-but there are several predefined ones in rdesigneur. All these define a
-spine with the following parameters:
-
-- head diameter 0.5 microns
-- head length 0.5 microns
-- shaft length 1 micron
-- shaft diameter of 0.2 microns
-- RM = 1.0 ohm-metre square
-- RA = 1.0 ohm-meter
-- CM = 0.01 Farads per square metre.
-
-Here are the predefined spine prototypes:
-
-- *make\_passive\_spine()*: This just makes a passive spine with the
- default parameters
-- *make\_exc\_spine()*: This makes a spine with NMDA and glu receptors,
- and also a calcium pool. The NMDA channel feeds the Ca pool.
-- *make\_active\_spine()*: This adds a Ca channel to the exc\_spine.
- and also a calcium pool.
-
-The spine distributions are specified in a familiar way for the first
-few arguments, and then there are multiple (optional) spine-specific
-parameters:
-
-*[spinename, region\_in\_cell, spacing, spacing\_distrib, size,
-size\_distrib, angle, angle\_distrib ]*
-
-Only the first two arguments are mandatory.
-
-- *spinename*: The prototype name
-- *region\_in\_cell*: Usual wildcard specification of names of
- compartments in which to put the spines.
-- *spacing*: Math expression to define spacing between spines. In the
- current implementation this evaluates to
- ``1/probability_of_spine_per_unit_length``. Defaults to 10 microns.
- Thus, there is a 10% probability of a spine insertion in every
- micron. This evaluation method has the drawback that it is possible
- to space spines rather too close to each other. If spacing is zero or
- less, no spines are inserted.
-- *spacing\_distrib*: Math expression for distribution of spacing. In
- the current implementation, this specifies the interval at which the
- system samples from the spacing probability above. Defaults to 1
- micron.
-- *size*: Linear scale factor for size of spine. All dimensions are
- scaled by this factor. The default spine head here is 0.5 microns in
- diameter and length. If the scale factor were to be 2, the volume
- would be 8 times as large. Defaults to 1.0.
-- *size\_distrib*: Range for size of spine. A random number R is
- computed in the range 0 to 1, and the final size used is
- ``size + (R - 0.5) * size_distrib``. Defaults to 0.5
-- *angle*: This specifies the initial angle at which the spine sticks
- out of the dendrite. If all angles were zero, they would all point
- away from the soma. Defaults to 0 radians.
-- *angle\_distrib*: Specifies a random number to add to the initial
- angle. Defaults to 2 PI radians, so the spines come out in any
- direction.
-
-One may well ask why we are not using a Python dictionary to handle all
-these parameters. Short answer is: terseness. Longer answer is that the
-rdesigneur format is itself meant to be an intermediate form for an
-eventual high-level, possibly XML-based multiscale modeling format.
-
-.. figure:: ../../images/rdes9_spiny_active.png
- :align: center
- :alt: 3-D display for spiny active neuron
-
- 3-D display for spiny active neuron
-Build a spiny neuron from a morphology file and put a reaction-diffusion system in it.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Rdesigneur is specially designed to take reaction systems with a
-dendrite, a spine head, and a spine PSD compartment, and embed these
-systems into neuronal morphologies. This example shows how this is done.
-
-The dendritic molecules diffuse along the dendrite in the region
-specified by the *chemDistrib* keyword. In this case they are placed on
-all apical and basal dendrites, but only at distances over 500 microns
-from the soma. The spine head and PSD reaction systems are inserted only
-into spines within this same *chemDistrib* zone. Diffusion coupling
-between dendrite, and each spine head and PSD is also set up. It takes a
-predefined chemical model file for Rdesigneur, which resides in the
-``./chem`` subdirectory. As in an earlier example, we turn off the
-electrical calculations here as they are not needed. Here we plot out
-the number of receptors on every single spine as a function of time.
-
-(stuff here)
-
-Make a full multiscale model with complex spiny morphology and electrical and chemical signaling.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-(stuff here)
diff --git a/moose-core/Docs/user/GUI/_templates/layout.html b/moose-core/Docs/user/GUI/_templates/layout.html
deleted file mode 100644
index 8eda056cde234f6d2ba16530e1fc06d5ec54d477..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/GUI/_templates/layout.html
+++ /dev/null
@@ -1,27 +0,0 @@
-{% extends "!layout.html" %}
-{% block sidebartitle %}
- {% if logo and theme_logo_only %}
- <a href="{{ pathto(master_doc) }}">
- {% else %}
- <a href="http://moose.ncbs.res.in/" class="icon icon-home"> {{ project }}
- {% endif %}
-
- {% if logo %}
- {# Not strictly valid HTML, but it's the only way to display/scale it properly, without weird scripting or heaps of work #}
- <img src="{{ pathto('_static/' + logo, 1) }}" class="logo" />
- {% endif %}
- </a>
- {% if theme_display_version %}
- {%- set nav_version = version %}
- {% if READTHEDOCS and current_version %}
- {%- set nav_version = current_version %}
- {% endif %}
- {% if nav_version %}
- <div class="version">
- {{ nav_version }}
- </div>
- {% endif %}
- {% endif %}
-
- {% include "searchbox.html" %}
-{% endblock %}
diff --git a/moose-core/Docs/user/GUI/conf.py b/moose-core/Docs/user/GUI/conf.py
deleted file mode 100644
index fc97e6f07d7c86fc4af5f5e2a67c1176e3254872..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/GUI/conf.py
+++ /dev/null
@@ -1,249 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# MOOSE documentation build configuration file, created by
-# sphinx-quickstart on Tue Jul 1 19:05:47 2014.
-#
-# This file is execfile()d with the current directory set to its containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-import sys, os
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('../../moose/moose-core/python'))
-
-# -- General configuration -----------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be extensions
-# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc',
- 'sphinx.ext.mathjax',
- 'sphinx.ext.autosummary',
- 'sphinx.ext.viewcode',
- 'numpydoc']
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix of source filenames.
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8-sig'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'MOOSE'
-copyright = u'2016'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '3.2'
-# The full version, including alpha/beta/rc tags.
-release = '3.2'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#language = None
-
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns = ['_build']
-
-# The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = True
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-
-# -- Options for HTML output ---------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages. See the documentation for
-# a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further. For a list of options available for each theme, see the
-# documentation.
-# html_theme_options = {'stickysidebar': 'true',
-# 'sidebarwidth': '300'}
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
-# The name for this set of Sphinx documents. If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-html_logo = '../../images/moose_logo.png'
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-#html_domain_indices = True
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
-
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it. The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'MOOSEdoc'
-
-
-# -- Options for LaTeX output --------------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
- ('index', 'MOOSE.tex', u'MOOSE Documentation',
- u'Upinder Bhalla, Aviral Goel and Harsha Rani', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-latex_logo = '../images/moose_logo.png'
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-latex_show_pagerefs = True
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-latex_domain_indices = True
-
-
-# -- Options for manual page output --------------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
- ('index', 'moose', u'MOOSE Documentation',
- [u'Upinder Bhalla, Aviral Goel and Harsha Rani'], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output ------------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-# dir menu entry, description, category)
-texinfo_documents = [
- ('index', 'MOOSE', u'MOOSE Documentation',
- u'Upinder Bhalla, Aviral Goel and Harsha Rani', 'MOOSE', 'MOOSE is the Multiscale Object-Oriented Simulation Environment.',
- 'Science'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-#numpydoc option
-numpydoc_show_class_members = True
diff --git a/moose-core/Docs/user/GUI/index.rst b/moose-core/Docs/user/GUI/index.rst
deleted file mode 100644
index 0af05af9b374ae5daf6fb34b229dd59ad1b8352c..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/GUI/index.rst
+++ /dev/null
@@ -1,21 +0,0 @@
-.. MOOSE documentation master file, created by
- sphinx-quickstart on Tue Jul 1 19:05:47 2014.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Gui documentation for MOOSE
-============================
-
-MOOSE is the Multiscale Object-Oriented Simulation Environment. It can do all these calculations together. One of its major uses is to make biologically detailed models that combine electrical and chemical signaling.
-This document describes the salient features of the GUI and Kinetickit of MOOSE
-
-Contents:
-
-.. toctree::
- :maxdepth: 2
- :numbered:
-
-
- MooseGuiDocs
- Kkit12Documentation
- RdesigneurDocumentation
diff --git a/moose-core/Docs/user/README.txt b/moose-core/Docs/user/README.txt
deleted file mode 100644
index 045a76268aedd8bc6710545d8e4481036cad0343..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/README.txt
+++ /dev/null
@@ -1,52 +0,0 @@
-This directory contains MOOSE user documentation.
-
-The documentation is encoded in the Markdown format. Each of the Markdown
-files is converted here to a corresponding HTML file for viewing in a browser,
-and can be converted to many other formats. To learn more about the Markdown
-format itself, go to the other 'markdown' directory one level up, in the
-main 'Docs' directory.
-
-Here are some of the important files:
- - index.html:
- If you just want to read the documentation, open this file in
- your browser, and start exploring! This file links to all the
- other user documents. All the user documents are listed below as
- well, as *.markdown files.
- - markdown/pymoose2walkthrough.markdown:
- "Getting started with python scripting for MOOSE"
- - markdown/MooseGuiDocs.markdown:
- "MOOSEGUI: Graphical interface for MOOSE"
- - markdown/Nkit2Documentation.markdown:
- "Neuronal simulations in MOOSEGUI". THIS IS CURRENTLY NOT INCLUDED
- - markdown/Kkit12Documentation.markdown:
- "Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI"
- - markdown/RdesigneurDocumentation:markdown:
- "Reaction Diffusion and Electrical SIGnaling in NEURons):Interface
- to the multiscale modeling capabilities in MOOSE"
- - markdown/moosebuiltindocs.markdown:
- "MOOSE class and function documentation"
- This file is auto-generated by the 'py/digestbuiltindocs.py'
- Python script (see below).
- - py/digestbuiltindocs.py: This Python script compiles all the inline
- documentation for MOOSE classes and functions, as visible in the
- MOOSE Python module, into a Markdown text file. THIS IS CURRENTLY
- BROKEN.
- - py/create_rest_doc.py: This Python script compiles all the inline
- documentation for MOOSE classes and functions, as visible in the
- MOOSE Python module, into a reST text file.
- - py/index.rst: This is the index file for use when building the Python
- docs using sphinx.
- - py/moose_builtins.rst: This is for sphinx to process the pymoose builtin
- doc strings (using autodoc extension)
- - py/moose_classes.rst: This is generated by running py/create_rest_doc.py
- and has the extracted inline documentation of MOOSE classes and
- their fields.
- - build: Shell script to do the necessary compilation and conversions.
-
---------------------------------------------------------------------------------
-N.B.: This text file has Windows-style line endings (CR/LF) for easy
-viewing in Windows. We will try to keep the other text files here
-Windows-compatible (e.g.: *.markdown files), but we may slip.
-If you have difficulty viewing them in Notepad, try the inbuilt Wordpad
-editor, or better still, download a good text editor like Notepad++ or Geany.
---------------------------------------------------------------------------------
diff --git a/moose-core/Docs/user/build b/moose-core/Docs/user/build
deleted file mode 100755
index 8a270293158aacdb01822322b8738e069f2bd3e0..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/build
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/bin/sh
-
-echo "[ Compiling inline docs ]"
-echo "digestbuiltindocs.py -> moosebuiltindocs.markdown"
-PYTHONPATH=../../python:$PYTHONPATH
-python py/digestbuiltindocs.py markdown/moosebuiltindocs.markdown > /dev/null
-
-echo "[ Generating HTML ]"
-echo "moosebuiltindocs.markdown -> moosebuiltindocs.html"
-pandoc \
- -c css/moosedocs.css \
- -c css/moosebuiltindocs.css \
- markdown/moosebuiltindocs.markdown -o html/moosebuiltindocs.html
-
-echo "index.markdown -> index.html"
-pandoc \
- -c html/css/moosedocs.css \
- markdown/index.markdown -o index.html
-
-echo "MooseGuiDocs.markdown -> MooseGuiDocs.html"
-pandoc \
- --toc \
- -c css/moosedocs.css \
- markdown/MooseGuiDocs.markdown -o html/MooseGuiDocs.html
-
-echo "Kkit12Documentation.markdown -> Kkit12Documentation.html"
-pandoc \
- --toc \
- -c css/moosedocs.css \
- markdown/Kkit12Documentation.markdown -o html/Kkit12Documentation.html
-
-echo "pymoose2walkthrough.markdown -> pymoose2walkthrough.html"
-pandoc \
- --toc \
- -c css/moosedocs.css \
- markdown/pymoose2walkthrough.markdown -o html/pymoose2walkthrough.html
-
-echo "Nkit2Documentation.markdown -> Nkit2Documentation.html"
-pandoc \
- --toc \
- -c css/moosedocs.css \
- markdown/Nkit2Documentation.markdown -o html/Nkit2Documentation.html
-
-# PDF: not tried yet.
-# echo "[ Generating PDF ]"
-# pandoc \
- # markdown/Nkit2Documentation.markdown -o pdf/Nkit2Documentation.pdf
-
-echo "[ Done! ]"
diff --git a/moose-core/Docs/user/html/Kkit12Documentation.html b/moose-core/Docs/user/html/Kkit12Documentation.html
deleted file mode 100644
index 95abd860d0b0947c8b02bc6cdb5eb2a261e87d2b..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/html/Kkit12Documentation.html
+++ /dev/null
@@ -1,311 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Style-Type" content="text/css" />
- <meta name="generator" content="pandoc" />
- <title></title>
- <style type="text/css">code{white-space: pre;}</style>
- <link rel="stylesheet" href="css/moosedocs.css" type="text/css" />
-</head>
-<body>
-<div id="TOC">
-<ul>
-<li><a href="#kinetikit-12-interface-for-chemical-kinetic-models-in-moosegui">Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI</a><ul>
-<li><a href="#upi-bhalla">Upi Bhalla</a></li>
-<li><a href="#harsha-rani">Harsha Rani</a><ul>
-<li><a href="#dec-27-2014">Dec 27, 2014</a></li>
-</ul></li>
-</ul></li>
-<li><a href="#introduction"><a href="#TOC">Introduction</a></a><ul>
-<li><a href="#todo-what-are-chemical-kinetic-models"><a href="#TOC"><strong>TODO</strong> What are chemical kinetic models?</a></a></li>
-<li><a href="#levels-of-model"><a href="#TOC">Levels of model</a></a></li>
-<li><a href="#numerical-methods"><a href="#TOC">Numerical methods</a></a></li>
-</ul></li>
-<li><a href="#using-kinetikit-12"><a href="#TOC">Using Kinetikit 12</a></a><ul>
-<li><a href="#overview"><a href="#TOC">Overview</a></a></li>
-<li><a href="#model-layout-and-icons"><a href="#TOC">Model layout and icons</a></a><ul>
-<li><a href="#compartment"><a href="#TOC">Compartment</a></a></li>
-<li><a href="#pool"><a href="#TOC">Pool</a></a></li>
-<li><a href="#buffered-pools"><a href="#TOC">Buffered pools</a></a></li>
-<li><a href="#reaction"><a href="#TOC">Reaction</a></a></li>
-<li><a href="#mass-action-enzymes"><a href="#TOC">Mass-action enzymes</a></a></li>
-<li><a href="#michaelis-menten-enzymes"><a href="#TOC">Michaelis-Menten Enzymes</a></a></li>
-<li><a href="#function"><a href="#TOC">Function</a></a></li>
-</ul></li>
-<li><a href="#model-operations"><a href="#TOC">Model operations</a></a></li>
-<li><a href="#model-building"><a href="#TOC">Model building</a></a></li>
-</ul></li>
-</ul>
-</div>
-<h1 id="kinetikit-12-interface-for-chemical-kinetic-models-in-moosegui"><a href="#kinetikit-12-interface-for-chemical-kinetic-models-in-moosegui">Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI</a></h1>
-<h2 id="upi-bhalla"><a href="#upi-bhalla">Upi Bhalla</a></h2>
-<h2 id="harsha-rani"><a href="#harsha-rani">Harsha Rani</a></h2>
-<h3 id="dec-27-2014"><a href="#dec-27-2014">Dec 27, 2014</a></h3>
-<ul>
-<li><p><a href="#introduction">Introduction</a></p></li>
-<li><a href="#todo-what-are-chemical-kinetic-models"><strong>TODO</strong> What are chemical kinetic models?</a>
-<ul>
-<li><a href="#levels-of-model">Levels of model</a></li>
-<li><a href="#numerical-methods">Numerical methods</a></li>
-</ul></li>
-<li><p><a href="#using-kinetikit-12">Using Kinetikit 12</a></p>
-<pre><code>* [Overview](#overview)</code></pre>
-<ul>
-<li><p><a href="#model-layout-and-icons">Model layout and icons</a></p>
-<pre><code> * [Compartment](#compartment)</code></pre>
-<ul>
-<li><a href="#pool">Pool</a></li>
-<li><a href="#buffered-pools">Buffered pools</a></li>
-<li><a href="#reaction">Reaction</a></li>
-<li><a href="#mass-action-enzymes">Mass-action enzymes</a></li>
-<li><a href="#michaelis-menten-enzymes">Michaelis-Menten Enzymes</a></li>
-<li><a href="#function">Function</a></li>
-</ul></li>
-<li><a href="#model-operations">Model operations</a></li>
-<li><p><a href="#model-building">Model Building</a></p></li>
-</ul></li>
-</ul>
-<h1 id="introduction"><a href="#introduction"><a href="#TOC">Introduction</a></a></h1>
-<p>Kinetikit 12 is a graphical interface for doing chemical kinetic modeling in MOOSE. It is derived in part from Kinetikit, which was the graphical interface used in GENESIS for similar models. Kinetikit, also known as kkit, was at version 11 with GENESIS. Here we start with Kinetikit 12.</p>
-<h2 id="todo-what-are-chemical-kinetic-models"><a href="#todo-what-are-chemical-kinetic-models"><a href="#TOC"><strong>TODO</strong> What are chemical kinetic models?</a></a></h2>
-<p>Much of neuronal computation occurs through chemical signaling. For example, many forms of synaptic plasticity begin with calcium influx into the synapse, followed by calcium binding to calmodulin, and then calmodulin activation of numerous enzymes. These events can be represented in chemical terms:</p>
-<blockquote>
-<p>4 Ca<sup>2+</sup> + CaM <===> Ca<sub>4</sub>.CaM</p>
-</blockquote>
-<p>Such chemical equations can be modeled through standard Ordinary Differential Equations, if we ignore space:</p>
-<blockquote>
-<p>d[Ca]/dt = −4K<sub>f</sub> ∗ [Ca]<sup>4</sup> ∗ [CaM] + 4K<sub>b</sub> ∗ [Ca<sub>4</sub>.CaM] d[CaM]/dt = −K<sub>f</sub> ∗ [Ca]<sup>4</sup> ∗ [CaM] + K<sub>b</sub> ∗ [Ca<sub>4</sub>.CaM] d[Ca4.CaM]/dt = K<sub>f</sub> ∗ [Ca]<sup>4</sup> ∗ [CaM] − K<sub>b</sub> ∗ [Ca<sub>4</sub>.CaM]</p>
-</blockquote>
-<p>MOOSE models these chemical systems. This help document describes how to do such modelling using the graphical interface, Kinetikit 12.</p>
-<h2 id="levels-of-model"><a href="#levels-of-model"><a href="#TOC">Levels of model</a></a></h2>
-<p>Chemical kinetic models can be simple well-stirred (or point) models, or they could have multiple interacting compartments, or they could include space explicitly using reaction-diffusion. In addition such models could be solved either deterministically, or using a stochastic formulation. At present Kinetikit handles compartmental models but does not compute diffusion within the compartments, though MOOSE itself can do this at the script level. Kkit12 will do deterministic as well as stochastic chemical calculations.</p>
-<h2 id="numerical-methods"><a href="#numerical-methods"><a href="#TOC">Numerical methods</a></a></h2>
-<ul>
-<li><strong>Deterministic</strong>: Adaptive timestep 5th order Runge-Kutta-Fehlberg from the GSL (GNU Scientific Library).</li>
-<li><strong>Stochastic</strong>: Optimized Gillespie Stochastic Systems Algorithm, custom implementation.</li>
-</ul>
-<h1 id="using-kinetikit-12"><a href="#using-kinetikit-12"><a href="#TOC">Using Kinetikit 12</a></a></h1>
-<h2 id="overview"><a href="#overview"><a href="#TOC">Overview</a></a></h2>
-<ul>
-<li>Load models using <strong><code>File -> Load model</code></strong>. A reaction schematic for the chemical system appears in the <strong><code>Editor view</code></strong> tab.</li>
-<li>View parameters in <strong><code>Editor view</code></strong> tab by clicking on icons, and looking at entries in <strong><code>Properties</code></strong> table to the right.</li>
-<li>Edit parameters by changing their values in the <strong><code>Properties</code></strong> table.</li>
-<li>From Run View, Pools can be plotted by clicking on their icons and dragging the icons onto the plot Window. Presently only concentration is plottable.</li>
-<li>Run models using <strong><code>Run</code></strong> button.</li>
-<li>Select numerical method using options under <strong><code>Preferences</code></strong> button in simulation control.</li>
-</ul>
-<p><!--* Save plots using the icons at the bottom of the <strong><code>Plot Window</code></strong>.</p>
-<p>Most of these operations are detailed in other sections, and are shared with other aspects of the MOOSE simulation interface. Here we focus on the Kinetikit-specific items.</p>
-<h2 id="model-layout-and-icons"><a href="#model-layout-and-icons"><a href="#TOC">Model layout and icons</a></a></h2>
-<p>When you are in the <strong><code>Model View</code></strong> tab you will see a collection of icons, arrows, and grey boxes surrounding these. This is a schematic of the reaction scheme being modeled. You can view and change parameters, and change the layout of the model.</p>
-<div class="figure">
-<img src="../../images/Moose1.png" />
-</div>
-<p>Resizing the model layout and icons:</p>
-<ul>
-<li><strong>Zoom</strong>: Comma and period keys. Alternatively, the mouse scroll wheel or vertical scroll line on the track pad will cause the display to zoom in and out.</li>
-<li><strong>Pan</strong>: The arrow keys move the display left, right, up, and down.</li>
-<li><strong>Entire Model View</strong>: Pressing the <strong><code>a</code></strong> key will fit the entire model into the entire field of view.</li>
-<li><strong>Resize Icons</strong>: Angle bracket keys, that is, <strong><code><</code></strong> and <strong><code>></code></strong> or <strong><code>+</code></strong> and <strong><code>-</code></strong>. This resizes the icons while leaving their positions on the screen layout more or less the same.</li>
-<li><strong>Original Model View</strong>: Presing the <strong><code>A</code></strong> key (capital <code>A</code>) will revert to the original model view including the original icon scaling.</li>
-</ul>
-<h3 id="compartment"><a href="#compartment"><a href="#TOC">Compartment</a></a></h3>
-<p>The <em>compartment</em> in moose is usually a contiguous domain in which a certain set of chemical reactions and molecular species occur. The definition is very closely related to that of a cell-biological compartment. Examples include the extracellular space, the cell membrane, the cytosol, and the nucleus. Compartments can be nested, but of course you cannot put a bigger compartment into a smaller one.</p>
-<ul>
-<li><strong>Icon</strong>: Grey boundary around a set of reactions.</li>
-<li><strong>Moving Compartments</strong>: Click and drag on the boundary.</li>
-<li><strong>Resizing Compartment boundary</strong>: Happens automatically when contents are repositioned, so that the boundary just contains contents.</li>
-<li><p><strong>Compartment editable parameters</strong>:</p>
-<ul>
-<li><strong><code>name</code></strong>: The name of the compartment.</li>
-<li><strong><code>size</code></strong>: This is the volume, surface area or length of the compartment, depending on its type.</li>
-</ul></li>
-<li><p><strong>Compartment fixed parameters</strong>:</p>
-<ul>
-<li><strong><code>numDimensions</code></strong>: This specifies whether the compartment is a volume, a 2-D surface, or if it is just being represented as a length.</li>
-</ul></li>
-</ul>
-<h3 id="pool"><a href="#pool"><a href="#TOC">Pool</a></a></h3>
-<p>This is the set of molecules of a given species within a compartment. Different chemical states of the same molecule are in different pools.</p>
-<ul>
-<li><strong>Icon</strong>: <img src="../../images/Pool.png" /> Colored rectangle with pool name in it.</li>
-<li><strong>Moving pools</strong>: Click and drag.</li>
-<li><p><strong>Pool editable parameters</strong>:</p>
-<ul>
-<li><strong><code>name</code></strong>: Name of the pool</li>
-<li><strong><code>n</code></strong>: Number of molecules in the pool</li>
-<li><strong><code>nInit</code></strong>: Initial number of molecules in the pool. <code>n</code> gets set to this value when the <code>reinit</code> operation is done.</li>
-<li><p><strong><code>conc</code></strong>: Concentration of the molecules in the pool.</p>
-<blockquote>
-<p>conc = n * unit_scale_factor / (N<sub>A</sub> * vol)</p>
-</blockquote></li>
-<li><p><strong><code>concInit</code></strong>: Initial concentration of the molecules in the pool.</p>
-<blockquote>
-<p>concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol) <code>conc</code> is set to this value when the <code>reinit</code> operation is done.</p>
-</blockquote></li>
-</ul></li>
-<li><p><strong>Pool fixed parameters</strong></p>
-<ul>
-<li><strong><code>size</code></strong>: Derived from the compartment that holds the pool. Specifies volume, surface area or length of the holding compartment.</li>
-</ul></li>
-</ul>
-<h3 id="buffered-pools"><a href="#buffered-pools"><a href="#TOC">Buffered pools</a></a></h3>
-<p>Some pools are set to a fixed <code>n</code>, that is number of molecules, and therefore a fixed concentration, throughout a simulation. These are buffered pools.</p>
-<ul>
-<li><strong>Icon</strong>: <img src="../../images/BufPool.png" /> Colored rectangle with pool name in it.</li>
-<li><strong>Moving Buffered pools</strong>: Click and drag.</li>
-<li><p><strong>Buffered Pool editable parameters</strong></p>
-<ul>
-<li><strong><code>name</code></strong>: Name of the pool</li>
-<li><strong><code>nInit</code></strong>: Fixed number of molecules in the pool. <code>n</code> gets set to this value throughout the run.</li>
-<li><p><strong><code>concInit</code></strong>: Fixed concentration of the molecules in the pool.</p>
-<blockquote>
-<p>concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol) <code>conc</code> is set to this value throughout the run.</p>
-</blockquote></li>
-</ul></li>
-<li><p><strong>Pool fixed parameters</strong>:</p>
-<ul>
-<li><strong><code>n</code></strong>: Number of molecules in the pool. Derived from <code>nInit</code>.</li>
-<li><strong><code>conc</code></strong>: Concentration of molecules in the pool. Derived from <code>concInit</code>.</li>
-<li><strong><code>size</code></strong>: Derived from the compartment that holds the pool. Specifies volume, surface area or length of the holding compartment.</li>
-</ul></li>
-</ul>
-<h3 id="reaction"><a href="#reaction"><a href="#TOC">Reaction</a></a></h3>
-<p>These are conversion reactions between sets of pools. They are reversible, but you can set either of the rates to zero to get irreversibility. In the illustration below, <strong><code>D</code></strong> and <strong><code>A</code></strong> are substrates, and <strong><code>B</code></strong> is the product of the reaction. This is indicated by the direction of the green arrow.</p>
-<div class="figure">
-<img src="../../images/KkitReaction.png" />
-</div>
-<ul>
-<li><strong>Icon</strong>: <img src="../../images/KkitReacIcon.png" /> Reversible reaction arrow.</li>
-<li><strong>Moving Reactions</strong>: Click and drag.</li>
-<li><p><strong>Reaction editable parameters</strong>:</p>
-<ul>
-<li><strong><code>name</code></strong>: Name of reaction</li>
-<li><strong><code>K</code><sub><code>f</code></sub></strong>: Forward rate of reaction, in <code>concentration/time</code> units. This is the normal way to express and manipulate the reaction rate.</li>
-<li><strong><code>k</code><sub><code>f</code></sub></strong>: Forward rate of reaction, in <code>number/time</code> units. This is used internally for computations, but is volume-dependent and should not be used to manipulate the reaction rate unless you really know what you are doing.</li>
-<li><strong><code>K</code><sub><code>b</code></sub></strong>: Backward rate of reaction, in <code>concentration/time</code> units. This is the normal way to express and manipulate the reaction rate.</li>
-<li><strong><code>k</code><sub><code>b</code></sub></strong>: Backward rate of reaction, in <code>number/time</code> units. This is used internally for computations, but is volume-dependent and should not be used to manipulate the reaction rate unless you really know what you are doing.</li>
-</ul></li>
-<li><p><strong>Reaction fixed parameters</strong>:</p>
-<ul>
-<li><strong><code>numProducts</code></strong>: Number of product molecules.</li>
-<li><strong><code>numSubstrates</code></strong>: Number of substrates molecules.</li>
-</ul></li>
-</ul>
-<h3 id="mass-action-enzymes"><a href="#mass-action-enzymes"><a href="#TOC">Mass-action enzymes</a></a></h3>
-<p>These are enzymes that model the chemical equations</p>
-<blockquote>
-<p>E + S <===> E.S —> E + P</p>
-</blockquote>
-<p>Note that the second reaction is irreversible. Note also that mass-action enzymes include a pool to represent the <strong><code>E.S</code></strong> (enzyme-substrate) complex. In the example below, the enzyme pool is named <strong><code>MassActionEnz</code></strong>, the substrate is <strong><code>C</code></strong>, and the product is <strong><code>E</code></strong>. The direction of the enzyme reaction is indicated by the red arrows.</p>
-<div class="figure">
-<img src="../../images/MassActionEnzReac.png" />
-</div>
-<ul>
-<li><p><strong>Icon</strong>: <img src="../../images/MassActionEnzIcon.png" /> Colored ellipse atop a small square. The ellipse represents the enzyme. The small square represents <strong><code>E.S</code></strong>, the enzyme-substrate complex. The ellipse icon has the same color as the enzyme pool <strong><code>E</code></strong>. It is connected to the enzyme pool <strong><code>E</code></strong> with a straight line of the same color.</p>
-<p>The ellipse icon sits on a continuous, typically curved arrow in red, from the substrate to the product.</p>
-<p>A given enzyme pool can have any number of enzyme activities, since the same enzyme might catalyze many reactions.</p></li>
-<li><strong>Moving Enzymes</strong>: Click and drag on the ellipse.</li>
-<li><p><strong>Enzyme editable parameters</strong></p>
-<ul>
-<li><strong><code>name</code></strong>: Name of enzyme.</li>
-<li><strong><code>K</code><sub><code>m</code></sub></strong>: Michaelis-Menten value for enzyme, in <code>concentration</code> units.</li>
-<li><strong><code>k</code><sub><code>cat</code></sub></strong>: Production rate of enzyme, in <code>1/time</code> units. Equal to <code>k</code><sub><code>3</code></sub>, the rate of the second, irreversible reaction.</li>
-<li><strong><code>k</code><sub><code>1</code></sub></strong>: Forward rate of the <strong><code>E+S</code></strong> reaction, in number and <code>1/time</code> units. This is what is used in the internal calculations.</li>
-<li><strong><code>k</code><sub><code>2</code></sub></strong>: Backward rate of the <strong><code>E+S</code></strong> reaction, in <code>1/time</code> units. Used in internal calculations.</li>
-<li><strong><code>k</code><sub><code>3</code></sub></strong>: Forward rate of the <strong><code>E.S —> E + P</code></strong> reaction, in <code>1/time</code> units. Equivalent to <code>k</code><sub><code>cat</code></sub>. Used in internal calculations.</li>
-<li><strong><code>ratio</code></strong>: This is equal to <code>k</code><sub><code>2</code></sub><code>/k</code><sub><code>3</code></sub>. Needed to define the internal rates in terms of <code>K</code><sub><code>m</code></sub> and <code>k</code><sub><code>cat</code></sub>. I usually use a value of 4.</li>
-</ul></li>
-<li><p><strong>Enzyme-substrate-complex editable parameters</strong>: These are identical to those of any other pool.</p>
-<ul>
-<li><strong><code>name</code></strong>: Name of the <strong><code>E.S</code></strong> complex. Defaults to <strong><code><enzymeName>_cplx</code></strong>.</li>
-<li><strong><code>n</code></strong>: Number of molecules in the pool</li>
-<li><strong><code>nInit</code></strong>: Initial number of molecules in the complex. <code>n</code> gets set to this value when the <code>reinit</code> operation is done.</li>
-<li><p><strong><code>conc</code></strong>: Concentration of the molecules in the pool.</p>
-<blockquote>
-<p>conc = n * unit_scale_factor / (N<sub>A</sub> * vol)</p>
-</blockquote></li>
-<li><p><strong><code>concInit</code></strong>: Initial concentration of the molecules in the pool.</p>
-<blockquote>
-<p>concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol) <code>conc</code> is set to this value when the <code>reinit</code> operation is done.</p>
-</blockquote></li>
-</ul></li>
-<li><p><strong>Enzyme-substrate-complex fixed parameters</strong>:</p>
-<ul>
-<li><strong><code>size</code></strong>: Derived from the compartment that holds the pool. Specifies volume, surface area or length of the holding compartment. Note that the Enzyme-substrate-complex is assumed to be in the same compartment as the enzyme molecule.</li>
-</ul></li>
-</ul>
-<h3 id="michaelis-menten-enzymes"><a href="#michaelis-menten-enzymes"><a href="#TOC">Michaelis-Menten Enzymes</a></a></h3>
-<p>These are enzymes that obey the Michaelis-Menten equation</p>
-<blockquote>
-<p>V = V<sub>max</sub> * [S] / ( K<sub>m</sub> + [S] ) = k<sub>cat</sub> * [Etot] * [S] / ( K<sub>m</sub> + [S] )</p>
-</blockquote>
-<p>where</p>
-<ul>
-<li><code>V</code><sub><code>max</code></sub> is the maximum rate of the enzyme</li>
-<li><code>[Etot]</code> is the total amount of the enzyme</li>
-<li><code>K</code><sub><code>m</code></sub> is the Michaelis-Menten constant</li>
-<li><code>S</code> is the substrate.</li>
-</ul>
-<p>Nominally these enzymes model the same chemical equation as the mass-action enzyme:</p>
-<blockquote>
-<p>E + S <===> E.S —> E + P</p>
-</blockquote>
-<p>but they make the assumption that the <strong><code>E.S</code></strong> is in a quasi-steady-state with <strong><code>E</code></strong> and <strong><code>S</code></strong>, and they also ignore sequestration of the enzyme into the complex. So there is no representation of the <strong><code>E.S</code></strong> complex. In the example below, the enzyme pool is named <strong><code>MM_Enz</code></strong>, the substrate is <strong><code>E</code></strong>, and the product is <strong><code>F</code></strong>. The direction of the enzyme reaction is indicated by the red arrows.</p>
-<div class="figure">
-<img src="../../images/MM_EnzReac.png" />
-</div>
-<ul>
-<li><strong>Icon</strong>: <img src="../../images/MM_EnzIcon.png" /> Colored ellipse. The ellipse represents the enzyme The ellipse icon has the same color as the enzyme <strong><code>MM_Enz</code></strong>. It is connected to the enzyme pool <strong><code>MM_Enz</code></strong> with a straight line of the same color. The ellipse icon sits on a continuous, typically curved arrow in red, from the substrate to the product. A given enzyme pool can have any number of enzyme activities, since the same enzyme might catalyze many reactions.</li>
-<li><strong>Moving Enzymes</strong>: Click and drag.</li>
-<li><p><strong>Enzyme editable parameters</strong>:</p>
-<ul>
-<li><strong><code>name</code></strong>: Name of enzyme.</li>
-<li><strong><code>K</code><sub><code>m</code></sub></strong>: Michaelis-Menten value for enzyme, in <code>concentration</code> units.</li>
-<li><strong><code>k</code><sub><code>cat</code></sub></strong>: Production rate of enzyme, in <code>1/time</code> units. Equal to <code>k</code><sub><code>3</code></sub>, the rate of the second, irreversible reaction.</li>
-</ul></li>
-</ul>
-<h3 id="function"><a href="#function"><a href="#TOC">Function</a></a></h3>
-<p>Function objects can be used to evaluate expressions with arbitrary number of variables and constants. We can assign expression of the form:</p>
-<p>f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP )</p>
-<p>where ci‘s are constants and xi‘s and yi‘s are variables.</p>
-<p>It can parse mathematical expression defining a function and evaluate it and/or its derivative for specified variable values. The variables can be input from other moose objects. In case of arbitrary variable names, the source message must have the variable name as the first argument.</p>
-<ul>
-<li><strong>Icon</strong>: Colored rectangle with pool name. This is <strong><code>Æ’</code></strong> in the example image below. The input pools <strong><code>A</code></strong> and <strong><code>B</code></strong> connect to the <strong>Æ’</strong> with blue arrows. The function ouput's to BuffPool</li>
-</ul>
-<h2 id="model-operations"><a href="#model-operations"><a href="#TOC">Model operations</a></a></h2>
-<ul>
-<li><strong>Loading models</strong>: <strong><code>File -> Load Model -> select from dialog</code></strong>. This operation makes the previously loaded model disable and loads newly selected models in <strong><code>Model View</code></strong></li>
-<li><strong>New</strong>: <strong><code>File -> New -> Model name</code></strong>. This opens a empty widget for model building</li>
-<li><strong>Saving models</strong>: <strong><code>File -> Save Model -> select from dialog</code></strong>.</li>
-<li><p><strong>Changing numerical methods</strong>: <strong><code>Preference->Chemical tab</code></strong> item from Simulation Control. Currently supports:</p>
-<ul>
-<li>Runge Kutta: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions.</li>
-<li>Gillespie: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up.</li>
-<li>Exponential Euler:This methods computes the solution of partial and ordinary differential equations.</li>
-</ul></li>
-</ul>
-<h2 id="model-building"><a href="#model-building"><a href="#TOC">Model building</a></a></h2>
-<div class="figure">
-<img src="../../images/chemical_CS.png" />
-</div>
-<ul>
-<li><p>The Edit Widget includes various menu options and model icons on the top.* Use the mouse buttton to click and drag icons from toolbar to Edit Widget, two things will happen, icon will appear in the editor widget and a object editor will pop up with lots of parameters with respect to moose object. Rules:</p>
-<pre><code>* Compartment has to be created firstly (At present only single compartment model is allowed)</code></pre>
-<ul>
-<li>Enzyme should be dropped on a pool as parent and function should be dropped on buffPool for output
-<li>
-Drag in pool's and reaction on to the editor widget, now one can set up a reaction.Click on mooseObject one can find a little arrow on the top right corner of the object, drag from this little arrow to any object for connection.E.g pool to reaction and reaction to pool. Specific connection type gets specific colored arrow. E.g. Green color arrow for specifying connection between reactant and product for reaction. Clicking on the object one can rearrange object for clean layout. Second order reaction can also be done by repeating the connection over again</li>
-</ul></li>
-<li><p>Each connection can be deleted and using rubberband selection each moose object can be deleted</p></li>
-</ul>
-<div class="figure">
-<img src="../../images/Chemical_run.png" />
-</div>
-<ul>
-<li>From run widget, pools are draggable to plot window for plotting. (Currently <strong><code>conc</code></strong> is plotted as default field) Plots are color-coded as per in model.</li>
-<li>Model can be run by clicking start button. One can stop button in mid-stream and start up again without affectiong the calculations. The reset button clears the simulation.</li>
-</ul>
-</body>
-</html>
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Style-Type" content="text/css" />
- <meta name="generator" content="pandoc" />
- <title></title>
- <style type="text/css">code{white-space: pre;}</style>
- <link rel="stylesheet" href="css/moosedocs.css" type="text/css" />
-</head>
-<body>
-<div id="TOC">
-<ul>
-<li><a href="#moose-gui"><strong>MOOSE GUI</strong></a><ul>
-<li><a href="#contents">Contents</a></li>
-<li><a href="#introduction">Introduction</a></li>
-<li><a href="#interface">Interface</a><ul>
-<li><a href="#menu-bar">Menu Bar</a></li>
-<li><a href="#editor-view">Editor View</a></li>
-<li><a href="#run-view">Run View</a></li>
-</ul></li>
-</ul></li>
-</ul>
-</div>
-<h1 id="moose-gui"><a href="#moose-gui"><strong>MOOSE GUI</strong></a></h1>
-<p><strong>Graphical interface for MOOSE</strong></p>
-<p><em>Harsha Rani, Aviral Goel, Upinder S. Bhalla</em></p>
-<hr />
-<h2 id="contents"><a href="#contents">Contents</a></h2>
-<ul>
-<li><a href="#introduction">Introduction</a></li>
-<li><a href="#interface">Interface</a>
-<ul>
-<li><a href="#menu-bar">Menu Bar</a>
-<ul>
-<li><a href="#menu-file">File</a>
-<ul>
-<li><a href="#file-new">New</a></li>
-<li><a href="#file-load-model">Load Model</a></li>
-<li><a href="#file-connect-biomodels">Connect BioModels</a></li>
-<li><a href="#file-quit">Quit</a></li>
-</ul></li>
-<li><a href="#menu-view">View</a>
-<ul>
-<li><a href="#editor-view">Editor View</a></li>
-<li><a href="#run-view">Run View</a></li>
-<li><a href="#dock-widgets">Dock Widgets</a></li>
-<li><a href="#subwindows">SubWindows</a></li>
-</ul></li>
-<li><a href="#menu-help">Help</a>
-<ul>
-<li><a href="#about-moose">About MOOSE</a></li>
-<li><a href="#built-in-documentation">Built-in Documentation</a></li>
-<li><a href="#report-a-bug">Report a bug</a></li>
-</ul></li>
-</ul></li>
-<li><a href="#editor-view">Editor View</a>
-<ul>
-<li><a href="#model-editor">Model Editor</a></li>
-<li><a href="#property-editor">Property Editor</a></li>
-</ul></li>
-<li><a href="#run-view">Run View</a>
-<ul>
-<li><a href="#simulation-controls">Simulation Controls</a></li>
-<li><a href="#plot-widget">Plot Widget</a>
-<ul>
-<li><a href="#plot-widget-toolbar">Toolbar</a></li>
-<li><a href="#plot-widget-context-menu">Context Menu</a></li>
-</ul></li>
-</ul></li>
-</ul></li>
-</ul>
-<h2 id="introduction"><a href="#introduction">Introduction</a></h2>
-<p>The Moose GUI lets you work on both <a href="Kkit12Documentation.html">chemical</a> and <a href="Nkit2Documentation.html">compartmental/electrical</a> neuronal models using a common interface. This document describes the salient features of the GUI</p>
-<h2 id="interface"><a href="#interface">Interface</a></h2>
-<p>The common interface layout consists of a a <a href="#menu-bar">menu bar</a> and two views, <a href="#editor-view">editor view</a> and <a href="#run-view">run view</a>.</p>
-<h3 id="menu-bar"><a href="#menu-bar">Menu Bar</a></h3>
-<div class="figure">
-<img src="../../images/MooseGuiMenuImage.png" />
-</div>
-<p>The menu bar appears at the top of the top of the main window. In Ubuntu 12.04, the menu bar appears only when the mouse is in the top menu strip of the screen. It consists of the following options -</p>
-<h4 id="file"><a href="#file">File</a></h4>
-<p>The File menu option provides the following sub options -</p>
-<ul>
-<li><a href="#file-new">New</a> - Create a new chemical signalling model.</li>
-<li><a href="#file-load-model">Load Model</a> - Load a chemical signalling or compartmental neuronal model from a file.</li>
-<li><a href="#recently-loaded-models">Recently Loaded Models</a> - List of models loaded in MOOSE.</li>
-<li><a href="#file-connect-biomodels">Connect BioModels</a> - Load chemical signaling models from the BioModels database.</li>
-<li><a href="#file-quit">Quit</a> - Quit the interface.</li>
-</ul>
-<h4 id="view"><a href="#view">View</a></h4>
-<p>View menu option provides the following sub options -</p>
-<ul>
-<li><a href="#editor-view">Editor View</a> - Switch to the editor view for editing models.</li>
-<li><a href="#run-view">Run View</a> - Switch to run view for running models.</li>
-<li><a href="#dock-widgets">Dock Widgets</a> - Following dock widgets are provided -
-<ul>
-<li><a href="#dock-widget-python">Python</a> - Brings up a full fledged python interpreter integrated with MOOSE GUI. You can interact with loaded models and load new models through the PyMoose API. The entire power of python language is accessible, as well as MOOSE-specific functions and classes.</li>
-<li><a href="#dock-widget-edit">Edit</a> - A property editor for viewing and editing the fields of a selected object such as a pool, enzyme, function or compartment. Editable field values can be changed by clicking on them and overwriting the new values. Please be sure to press enter once the editing is complete, in order to save your changes.</li>
-</ul></li>
-<li><a href="#subwindows">SubWindows</a> - This allows you to tile or tabify the run and editor views.</li>
-</ul>
-<h4 id="help"><a href="#help">Help</a></h4>
-<ul>
-<li><a href="#about-moose">About Moose</a> - Version and general information about MOOSE.</li>
-<li><a href="#butilt-in-documentation">Built-in documentation</a> - Documentation of MOOSE GUI.</li>
-<li><a href="#report-a-bug">Report a bug</a> - Directs to the SourceForge bug tracker for reporting bugs.</li>
-</ul>
-<h3 id="editor-view"><a href="#editor-view">Editor View</a></h3>
-<p>The editor view provides two windows -</p>
-<ul>
-<li><a href="#model-editor">Model Editor</a> - The model editor is a workspace to edit and create models. Using click-and-drag from the icons in the menu bar, you can create model entities such as chemical pools, reactions, and so on. A click on any object brings its property editor on screen (see below). In objects that can be interconnected, a click also brings up a special arrow icon that is used to connect objects together with messages. You can move objects around within the edit window using click-and-drag. Finally, you can delete objects by selecting one or more, and then choosing the delete option from the pop-up menu. When displaying a neuronal model, most of the editing options are disabled. However, you can still click on a dendrite in order to bring up the property editor.</li>
-</ul>
-<p>The Model Editor is different for chemical signalling and compartmental neuronal models. The links below the screenshots point to the details for the respective editors.</p>
-<div class="figure">
-<img src="../../images/ChemicalSignallingEditor.png" alt="Chemical Signalling Model Editor" /><p class="caption">Chemical Signalling Model Editor</p>
-</div>
-<div class="figure">
-<img src="../../images/CompartmentalEditor.png" alt="Compartmental Model Editor" /><p class="caption">Compartmental Model Editor</p>
-</div>
-<ul>
-<li><a href="#property-editor">Property Editor</a> - The property editor provides a way of viewing and editing the properties of objects selected in the model editor.</li>
-</ul>
-<div class="figure">
-<img src="../../images/PropertyEditor.png" alt="Property Editor" /><p class="caption">Property Editor</p>
-</div>
-<h3 id="run-view"><a href="#run-view">Run View</a></h3>
-<p>The Run view, as the name suggests, puts the GUI into a mode where the model can be simulated. As a first step in this, you can click-and-drag an object to the graph window in order to create a time-series plot for that object. For example, in a chemical reaction, you could drag a pool into the graph window and subsequent simulations will display a graph of the concentration of the pool as a function of time. Within the Run View window, the time-evolution of the simulation is displayed as an animation. For chemical kinetic models, the size of the icons for reactant pools scale to indicate concentration. For neuronal models, the colour of dendritic segments changes to indicate membrane potential. Above the Run View window, there is a special tool bar with a set of simulation controls to run the simulation.</p>
-<h4 id="simulation-controls"><a href="#simulation-controls">Simulation Controls</a></h4>
-<div class="figure">
-<img src="../../images/SimulationControl.png" alt="Simulation Control" /><p class="caption">Simulation Control</p>
-</div>
-<p>This panel allows you to control the various aspects of the simulation.</p>
-<ul>
-<li><a href="#run-time">Run Time</a> - Determines duration for which simulation is to run. A simulation which has already run, runs further for the specified additional period.</li>
-<li><a href="#reset">Reset</a> - Restores simulation to its initial state; re-initializes all variables to t = 0.</li>
-<li><a href="#stop">Stop</a> - This button halts an ongoing simulation.</li>
-<li><a href="#current-time">Current time</a> - This reports the current simulation time.</li>
-<li><a href="#preferences">Preferences</a> - Allows you to set simulation and visualization related preferences.</li>
-</ul>
-<h4 id="plot-widget"><a href="#plot-widget">Plot Widget</a></h4>
-<h5 id="toolbar"><a href="#toolbar">Toolbar</a></h5>
-<p>On top of plot window there is a little row of icons:</p>
-<div class="figure">
-<img src="../../images/PlotWindowIcons.png" />
-</div>
-<p>These are the plot controls. If you hover the mouse over them for a few seconds, a tooltip pops up. The icons represent the following functions:</p>
-<ul>
-<li><p><img src="../../images/Addgraph.png" /> - Add a new plot window</p></li>
-<li><p><img src="../../images/delgraph.png" /> - Deletes current plot window</p></li>
-<li><p><img src="../../images/grid.png" /> - Toggle X-Y axis grid</p></li>
-<li><p><img src="../../images/MatPlotLibHomeIcon.png" /> - Returns the plot display to its default position</p></li>
-<li><p><img src="../../images/MatPlotLibDoUndo.png" /> - Undoes or re-does manipulations you have done to the display.</p></li>
-<li><p><img src="../../images/MatPlotLibPan.png" /> - The plots will pan around with the mouse when you hold the left button down. The plots will zoom with the mouse when you hold the right button down.</p></li>
-<li><p><img src="../../images/MatPlotLibZoom.png" /> - With the <strong><code>left mouse button</code></strong>, this will zoom in to the specified rectangle so that the plots become bigger. With the <strong><code>right mouse button</code></strong>, the entire plot display will be shrunk to fit into the specified rectangle.</p></li>
-<li><p><img src="../../images/MatPlotLibConfigureSubplots.png" /> - You don't want to mess with these .</p></li>
-<li><p><img src="../../images/MatPlotLibSave.png" /> - Save the plot.</p></li>
-</ul>
-<h5 id="context-menu"><a href="#context-menu">Context Menu</a></h5>
-<p>The context menu is enabled by right clicking on the plot window. It has the following options -</p>
-<ul>
-<li><strong>Export to CSV</strong> - Exports the plotted data to CSV format</li>
-<li><strong>Toggle Legend</strong> - Toggles the plot legend</li>
-<li><strong>Remove</strong> - Provides a list of plotted entities. The selected entity will not be plotted.</li>
-</ul>
-</body>
-</html>
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Style-Type" content="text/css" />
- <meta name="generator" content="pandoc" />
- <title></title>
- <style type="text/css">code{white-space: pre;}</style>
- <link rel="stylesheet" href="css/moosedocs.css" type="text/css" />
-</head>
-<body>
-<div id="TOC">
-<ul>
-<li><a href="#introduction">Introduction</a></li>
-<li><a href="#neuronal-models">Neuronal models</a></li>
-<li><a href="#neuronal-simulations-in-moosegui">Neuronal simulations in MOOSEGUI</a><ul>
-<li><a href="#quick-start">Quick start</a><ul>
-<li><a href="#editor-view">Editor View</a></li>
-<li><a href="#run-view">Run View</a></li>
-</ul></li>
-<li><a href="#modeling-details">Modeling details</a></li>
-<li><a href="#demos">Demos</a></li>
-</ul></li>
-</ul>
-</div>
-<h1 id="introduction"><a href="#introduction">Introduction</a></h1>
-<p>Neuronal models in NeuroML 1.8 format can be loaded and simulated in the <strong>MOOSE Graphical User Interface</strong>. The GUI displays the neurons in 3D, and allows visual selection and editing of neuronal properties. Plotting and visualization of activity proceeds concurrently with the simulation. Support for creating and editing channels, morphology and networks is planned for the future.</p>
-<h1 id="neuronal-models"><a href="#neuronal-models">Neuronal models</a></h1>
-<p>Neurons are modeled as equivalent electrical circuits. The morphology of a neuron can be broken into isopotential compartments connected by axial resistances <code>R</code><sub><code>a</code></sub> denoting the cytoplasmic resistance. In each compartment, the neuronal membrane is represented as a capacitance <code>C</code><sub><code>m</code></sub> with a shunt leak resistance <code>R</code><sub><code>m</code></sub>. Electrochemical gradient (due to ion pumps) across the leaky membrane causes a voltage drive <code>E</code><sub><code>m</code></sub>, that hyperpolarizes the inside of the cell membrane compared to the outside.</p>
-<p>Each voltage dependent ion channel, present on the membrane, is modeled as a voltage dependent conductance <code>G</code><sub><code>k</code></sub> with gating kinetics, in series with an electrochemical voltage drive (battery) <code>E</code><sub><code>k</code></sub>, across the membrane capacitance <code>C</code><sub><code>m</code></sub>, as in the figure below.</p>
-<hr />
-<div class="figure">
-<img src="../../images/neuroncompartment.png" alt="Equivalent circuit of neuronal compartments" /><p class="caption"><strong>Equivalent circuit of neuronal compartments</strong></p>
-</div>
-<hr />
-<p>Neurons fire action potentials / spikes (sharp rise and fall of membrane potential <code>V</code><sub><code>m</code></sub>) due to voltage dependent channels. These result in opening of excitatory / inhibitory synaptic channels (conductances with batteries, similar to voltage gated channels) on other connected neurons in the network.</p>
-<p>MOOSE can handle large networks of detailed neurons, each with complicated channel dynamics. Further, MOOSE can integrate chemical signaling with electrical activity. Presently, creating and simulating these requires PyMOOSE scripting, but these will be incorporated into the GUI in the future.</p>
-<p>To understand channel kinetics and neuronal action potentials, run the Squid Axon demo installed along with MOOSEGUI and consult its help/tutorial.</p>
-<p>Read more about compartmental modeling in the first few chapters of the <a href="http://www.genesis-sim.org/GENESIS/iBoG/iBoGpdf/index.html">Book of Genesis</a>.</p>
-<p>Models can be defined in <a href="http://www.neuroml.org">NeuroML</a>, an XML format which is well supported across simulators. Channels, neuronal morphology (compartments), and networks can be specified using various levels of NeuroML, namely ChannelML, MorphML and NetworkML. Importing of cell models in the <a href="http://www.genesis-sim.org/GENESIS">GENESIS</a> <code>.p</code> format is supported for backwards compatibitility.</p>
-<h1 id="neuronal-simulations-in-moosegui"><a href="#neuronal-simulations-in-moosegui">Neuronal simulations in MOOSEGUI</a></h1>
-<h2 id="quick-start"><a href="#quick-start">Quick start</a></h2>
-<ul>
-<li>MOOSEGUI provides a few neuronal models in moose/Demos directory in user's home folder. For example, <em>File->Load</em> <code>~/moose/Demos/neuroml/PurkinjeCellPassive/PurkinjePassive.net.xml</code>, which is a model of the purkinje cell. A 3D rendering of the neuron appears in <strong><code>Editor</code></strong> tab.</li>
-<li>Click and drag to rotate, scroll wheel to zoom, and arrow keys to pan the 3D rendering.</li>
-<li>Click to select a compartment on the 3D model. The selected compartment is colored green.</li>
-<li>An editor will appear on the right hand side where the properties of the compartment can be edited.</li>
-<li>The 3D view of the model provided by the editor allows only editing of the compartment parameters.</li>
-<li>In the <strong><code>Run</code></strong> tab you can see two subwindows. The one on the left provides a dynamic visualization of the compartment Vm as the simulation progresses. The one on the right is the plot window where you can plot the Vm of the various compartments.</li>
-<li>Press <code>Ctrl</code> and click and drag a compartment from the visualizer to the plot window.</li>
-<li>Run the model using <strong><code>Run</code></strong> button. You can see the colors of the compartments changing as the simulation progresses. The graphs gets updated simultaneously with the visualizer.</li>
-</ul>
-<h3 id="editor-view"><a href="#editor-view">Editor View</a></h3>
-<div class="figure">
-<img src="../../images/NeurokitEditor.png" alt="Editor View" /><p class="caption"><strong>Editor View</strong></p>
-</div>
-<h3 id="run-view"><a href="#run-view">Run View</a></h3>
-<div class="figure">
-<img src="../../images/NeurokitRunner.png" alt="Run View" /><p class="caption"><strong>Run View</strong></p>
-</div>
-<h2 id="modeling-details"><a href="#modeling-details">Modeling details</a></h2>
-<p>MOOSE uses SI units throughout.</p>
-<p>Some salient properties of neuronal building blocks in MOOSE are described below. Variables that are updated at every simulation time step are are listed <strong>dynamical</strong>. Rest are parameters.</p>
-<ul>
-<li><p><strong>Compartment</strong><br /> When you select a compartment, you can view and edit its properties in the right pane. <code>V</code><sub><code>m</code></sub> and <code>I</code><sub><code>m</code></sub> are plot-able.</p>
-<ul>
-<li><strong><code>V</code><sub><code>m</code></sub></strong> : <strong>dynamical</strong> membrane potential (across <code>C</code><sub><code>m</code></sub>) in Volts.</li>
-<li><strong><code>C</code><sub><code>m</code></sub></strong> : membrane capacitance in Farads.</li>
-<li><strong><code>E</code><sub><code>m</code></sub></strong> : membrane leak potential in Volts due to the electrochemical gradient setup by ion pumps.</li>
-<li><strong><code>I</code><sub><code>m</code></sub></strong> : <strong>dynamical</strong> current in Amperes across the membrane via leak resistance <code>R</code><sub><code>m</code></sub>.</li>
-<li><strong><code>inject</code></strong> : current in Amperes injected externally into the compartment.</li>
-<li><strong><code>initVm</code></strong> : initial <code>V</code><sub><code>m</code></sub> in Volts.</li>
-<li><strong><code>R</code><sub><code>m</code></sub></strong> : membrane leak resistance in Ohms due to leaky channels.</li>
-<li><strong><code>diameter</code></strong> : diameter of the compartment in metres.</li>
-<li><strong><code>length</code></strong> : length of the compartment in metres.</li>
-</ul>
-<p>After selecting a compartment, you can click <strong><code>See children</code></strong> on the right pane to list its membrane channels, Ca pool, etc.</p></li>
-<li><p><strong>HHChannel</strong><br /> Hodgkin-Huxley channel with voltage dependent dynamical gates.</p>
-<ul>
-<li><strong><code>Gbar</code></strong> : peak channel conductance in Siemens.</li>
-<li><strong><code>E</code><sub><code>k</code></sub></strong> : reversal potential of the channel, due to electrochemical gradient of the ion(s) it allows.</li>
-<li><p><strong><code>G</code><sub><code>k</code></sub></strong> : <strong>dynamical</strong> conductance of the channel in Siemens.</p>
-<blockquote>
-<p>G<sub>k</sub>(t) = Gbar × X(t)<sup>Xpower</sup> × Y(t)<sup>Ypower</sup> × Z(t)<sup>Zpower</sup></p>
-</blockquote></li>
-<li><p><strong><code>I</code><sub><code>k</code></sub></strong> : <strong>dynamical</strong> current through the channel into the neuron in Amperes.</p>
-<blockquote>
-<p>I<sub>k</sub>(t) = G<sub>k</sub>(t) × (E<sub>k</sub>-V<sub>m</sub>(t))</p>
-</blockquote></li>
-<li><p><strong><code>X</code></strong>, <strong><code>Y</code></strong>, <strong><code>Z</code></strong> : <strong>dynamical</strong> gating variables (range <code>0.0</code> to <code>1.0</code>) that may turn on or off as voltage increases with different time constants.</p>
-<blockquote>
-<p>dX(t)/dt = X<sub>inf</sub>/Ï„ - X(t)/Ï„</p>
-</blockquote>
-Here, <code>X</code><sub><code>inf</code></sub> and <code>τ</code> are typically sigmoidal/linear/linear-sigmoidal functions of membrane potential <code>V</code><sub><code>m</code></sub>, which are described in a ChannelML file and presently not editable from MOOSEGUI. Thus, a gate may open <code>(X</code><sub><code>inf</code></sub><code>(V</code><sub><code>m</code></sub><code>) → 1)</code> or close <code>(X</code><sub><code>inf</code></sub><code>(V</code><sub><code>m</code></sub><code>) → 0)</code> on increasing <code>V</code><sub><code>m</code></sub>, with time constant <code>τ(V</code><sub><code>m</code></sub><code>)</code>.</li>
-<li><p><strong><code>Xpower</code></strong>, <strong><code>Ypower</code></strong>, <strong><code>Zpower</code></strong> : powers to which gates are raised in the <code>G</code><sub><code>k</code></sub><code>(t)</code> formula above.</p></li>
-</ul></li>
-<li><p><strong>HHChannel2D</strong><br /> The Hodgkin-Huxley channel2D can have the usual voltage dependent dynamical gates, and also gates that dependent on voltage and an ionic concentration, as for say Ca-dependent K conductance. It has the properties of HHChannel above, and a few more like <code>Xindex</code> as in the <a href="http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-26.html#ss26.61">GENESIS tab2Dchannel reference</a>.</p></li>
-<li><strong>CaConc</strong><br /> This is a pool of Ca ions in each compartment, in a shell volume under the cell membrane. The dynamical Ca concentration increases when Ca channels open, and decays back to resting with a specified time constant Ï„. Its concentration controls Ca-dependent K channels, etc.
-<ul>
-<li><p><code>Ca</code> : <strong>dynamical</strong> Ca concentration in the pool in units <code>mM</code> ( i.e., <code>mol/m</code><sup><code>3</code></sup>).</p>
-<blockquote>
-<p>d[Ca<sup>2+</sup>]/dt = B × I<sub>Ca</sub> - [Ca<sup>2+</sup>]/τ</p>
-</blockquote></li>
-<li><code>CaBasal</code>/<code>Ca_base</code> : Base Ca concentration to which the Ca decays</li>
-<li><code>tau</code> : time constant with which the Ca concentration decays to the base Ca level.</li>
-<li><code>B</code> : constant in the <code>[Ca</code><sup><code>2+</code></sup><code>]</code> equation above.</li>
-<li><p><code>thick</code> : thickness of the Ca shell within the cell membrane which is used to calculate <code>B</code> (see Chapter 19 of <a href="http://www.genesis-sim.org/GENESIS/iBoG/iBoGpdf/index.html">Book of GENESIS</a>.)</p></li>
-</ul></li>
-</ul>
-<h2 id="demos"><a href="#demos">Demos</a></h2>
-<ul>
-<li><p><strong>Cerebellar granule cell</strong><br /> <strong><code>File -> Load -></code></strong> <code>~/moose/Demos/neuroml/GranuleCell/GranuleCell.net.xml</code><br /> This is a single compartment Cerebellar granule cell with a variety of channels <a href="http://www.tnb.ua.ac.be/models/network.shtml">Maex, R. and De Schutter, E., 1997</a> (exported from <a href="http://www.neuroconstruct.org/">http://www.neuroconstruct.org/</a>). Click on its soma, and <strong>See children</strong> for its list of channels. Vary the <code>Gbar</code> of these channels to obtain regular firing, adapting and bursty behaviour (may need to increase tau of the Ca pool).</p></li>
-<li><p><strong>Purkinje cell</strong><br /> <strong><code>File -> Load -></code></strong> <code>~/moose/Demos/neuroml/PurkinjeCell/Purkinje.net.xml</code><br /> This is a purely passive cell, but with extensive morphology [De Schutter, E. and Bower, J. M., 1994] (exported from <a href="http://www.neuroconstruct.org/">http://www.neuroconstruct.org/</a>). The channel specifications are in an obsolete ChannelML format which MOOSE does not support.</p></li>
-<li><p><strong>Olfactory bulb subnetwork</strong><br /> <strong><code>File -> Load -></code></strong> <code>~/moose/Demos/neuroml/OlfactoryBulb/numgloms2_seed100.0_decimated.xml</code><br /> This is a pruned and decimated version of a detailed network model of the Olfactory bulb [Gilra A. and Bhalla U., in preparation] without channels and synaptic connections. We hope to post the ChannelML specifications of the channels and synapses soon.</p></li>
-<li><p><strong>All channels cell</strong><br /> <strong><code>File -> Load -></code></strong> <code>~/moose/Demos/neuroml/allChannelsCell/allChannelsCell.net.xml</code><br /> This is the Cerebellar granule cell as above, but with loads of channels from various cell types (exported from <a href="http://www.neuroconstruct.org/">http://www.neuroconstruct.org/</a>). Play around with the channel properties to see what they do. You can also edit the ChannelML files in <code>~/moose/Demos/neuroml/allChannelsCell/cells_channels/</code> to experiment further.</p></li>
-<li><p><strong>NeuroML python scripts</strong><br /> In directory <code>~/moose/Demos/neuroml/GranuleCell</code>, you can run <code>python FvsI_Granule98.py</code> which plots firing rate vs injected current for the granule cell. Consult this python script to see how to read in a NeuroML model and to set up simulations. There are ample snippets in <code>~/moose/Demos/snippets</code> too.</p></li>
-</ul>
-</body>
-</html>
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-<h1 class="title">Documentation for all MOOSE classes and functions</h1>
-<h2 class="author">As visible in the Python module</h2>
-<h3 class="date">Auto-generated on January 07, 2013</h3>
-</div>
-<h1 id="index-for-moose-classes">Index for MOOSE Classes</h1>
-<table>
-<tbody>
-<tr class="odd">
-<td align="left"><strong>A</strong></td>
-<td align="left"><a href="#enz"><code>Enz</code></a></td>
-<td align="left"><a href="#interpol2d"><code>Interpol2D</code></a></td>
-<td align="left"><a href="#nmdachan"><code>NMDAChan</code></a></td>
-<td align="left"><a href="#species"><code>Species</code></a></td>
-<td align="left"><a href="#vectortable"><code>VectorTable</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#adaptor"><code>Adaptor</code></a></td>
-<td align="left"><a href="#enzbase"><code>EnzBase</code></a></td>
-<td align="left"><a href="#intfire"><code>IntFire</code></a></td>
-<td align="left"><strong>O</strong></td>
-<td align="left"><a href="#spherepanel"><code>SpherePanel</code></a></td>
-<td align="left"><strong>Z</strong></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#annotator"><code>Annotator</code></a></td>
-<td align="left"><strong>F</strong></td>
-<td align="left"><a href="#izhikevichnrn"><code>IzhikevichNrn</code></a></td>
-<td align="left"><a href="#onetoallmsg"><code>OneToAllMsg</code></a></td>
-<td align="left"><a href="#spikegen"><code>SpikeGen</code></a></td>
-<td align="left"><a href="#zbufpool"><code>ZBufPool</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#arith"><code>Arith</code></a></td>
-<td align="left"><a href="#finfo"><code>Finfo</code></a></td>
-<td align="left"><strong>L</strong></td>
-<td align="left"><a href="#onetoonemsg"><code>OneToOneMsg</code></a></td>
-<td align="left"><a href="#stats"><code>Stats</code></a></td>
-<td align="left"><a href="#zenz"><code>ZEnz</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><strong>B</strong></td>
-<td align="left"><a href="#funcbase"><code>FuncBase</code></a></td>
-<td align="left"><a href="#leakyiaf"><code>LeakyIaF</code></a></td>
-<td align="left"><strong>P</strong></td>
-<td align="left"><a href="#stimulustable"><code>StimulusTable</code></a></td>
-<td align="left"><a href="#zfuncpool"><code>ZFuncPool</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#boundary"><code>Boundary</code></a></td>
-<td align="left"><a href="#funcpool"><code>FuncPool</code></a></td>
-<td align="left"><strong>M</strong></td>
-<td align="left"><a href="#panel"><code>Panel</code></a></td>
-<td align="left"><a href="#stoich"><code>Stoich</code></a></td>
-<td align="left"><a href="#zmmenz"><code>ZMMenz</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#bufpool"><code>BufPool</code></a></td>
-<td align="left"><strong>G</strong></td>
-<td align="left"><a href="#markovchannel"><code>MarkovChannel</code></a></td>
-<td align="left"><a href="#pidcontroller"><code>PIDController</code></a></td>
-<td align="left"><a href="#stoichcore"><code>StoichCore</code></a></td>
-<td align="left"><a href="#zombiebufpool"><code>ZombieBufPool</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><strong>C</strong></td>
-<td align="left"><a href="#geometry"><code>Geometry</code></a></td>
-<td align="left"><a href="#markovgslsolver"><code>MarkovGslSolver</code></a></td>
-<td align="left"><a href="#pool"><code>Pool</code></a></td>
-<td align="left"><a href="#stoichpools"><code>StoichPools</code></a></td>
-<td align="left"><a href="#zombiecaconc"><code>ZombieCaConc</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#caconc"><code>CaConc</code></a></td>
-<td align="left"><a href="#ghk"><code>GHK</code></a></td>
-<td align="left"><a href="#markovratetable"><code>MarkovRateTable</code></a></td>
-<td align="left"><a href="#poolbase"><code>PoolBase</code></a></td>
-<td align="left"><a href="#sumfunc"><code>SumFunc</code></a></td>
-<td align="left"><a href="#zombiecompartment"><code>ZombieCompartment</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#chanbase"><code>ChanBase</code></a></td>
-<td align="left"><a href="#group"><code>Group</code></a></td>
-<td align="left"><a href="#markovsolver"><code>MarkovSolver</code></a></td>
-<td align="left"><a href="#port"><code>Port</code></a></td>
-<td align="left"><a href="#surface"><code>Surface</code></a></td>
-<td align="left"><a href="#zombieenz"><code>ZombieEnz</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#chemmesh"><code>ChemMesh</code></a></td>
-<td align="left"><a href="#gslintegrator"><code>GslIntegrator</code></a></td>
-<td align="left"><a href="#markovsolverbase"><code>MarkovSolverBase</code></a></td>
-<td align="left"><a href="#pulsegen"><code>PulseGen</code></a></td>
-<td align="left"><a href="#symcompartment"><code>SymCompartment</code></a></td>
-<td align="left"><a href="#zombiefuncpool"><code>ZombieFuncPool</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#cinfo"><code>Cinfo</code></a></td>
-<td align="left"><a href="#gslstoich"><code>GslStoich</code></a></td>
-<td align="left"><a href="#mathfunc"><code>MathFunc</code></a></td>
-<td align="left"><strong>R</strong></td>
-<td align="left"><a href="#synapse"><code>Synapse</code></a></td>
-<td align="left"><a href="#zombiehhchannel"><code>ZombieHHChannel</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#clock"><code>Clock</code></a></td>
-<td align="left"><a href="#gssastoich"><code>GssaStoich</code></a></td>
-<td align="left"><a href="#mdouble"><code>Mdouble</code></a></td>
-<td align="left"><a href="#rc"><code>RC</code></a></td>
-<td align="left"><a href="#synbase"><code>SynBase</code></a></td>
-<td align="left"><a href="#zombiemmenz"><code>ZombieMMenz</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#compartment"><code>Compartment</code></a></td>
-<td align="left"><strong>H</strong></td>
-<td align="left"><a href="#meshentry"><code>MeshEntry</code></a></td>
-<td align="left"><a href="#reac"><code>Reac</code></a></td>
-<td align="left"><a href="#synchan"><code>SynChan</code></a></td>
-<td align="left"><a href="#zombiepool"><code>ZombiePool</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#cplxenzbase"><code>CplxEnzBase</code></a></td>
-<td align="left"><a href="#hdf5datawriter"><code>HDF5DataWriter</code></a></td>
-<td align="left"><a href="#mgblock"><code>MgBlock</code></a></td>
-<td align="left"><a href="#reacbase"><code>ReacBase</code></a></td>
-<td align="left"><a href="#synchanbase"><code>SynChanBase</code></a></td>
-<td align="left"><a href="#zombiereac"><code>ZombieReac</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#cubemesh"><code>CubeMesh</code></a></td>
-<td align="left"><a href="#hdf5writerbase"><code>HDF5WriterBase</code></a></td>
-<td align="left"><a href="#mmenz"><code>MMenz</code></a></td>
-<td align="left"><a href="#rectpanel"><code>RectPanel</code></a></td>
-<td align="left"><strong>T</strong></td>
-<td align="left"><a href="#zombiesumfunc"><code>ZombieSumFunc</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#cylmesh"><code>CylMesh</code></a></td>
-<td align="left"><a href="#hemispherepanel"><code>HemispherePanel</code></a></td>
-<td align="left"><a href="#msg"><code>Msg</code></a></td>
-<td align="left"><a href="#reducemsg"><code>ReduceMsg</code></a></td>
-<td align="left"><a href="#table"><code>Table</code></a></td>
-<td align="left"><a href="#zpool"><code>ZPool</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#cylpanel"><code>CylPanel</code></a></td>
-<td align="left"><a href="#hhchannel"><code>HHChannel</code></a></td>
-<td align="left"><a href="#mstring"><code>Mstring</code></a></td>
-<td align="left"><strong>S</strong></td>
-<td align="left"><a href="#tablebase"><code>TableBase</code></a></td>
-<td align="left"><a href="#zreac"><code>ZReac</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><strong>D</strong></td>
-<td align="left"><a href="#hhchannel2d"><code>HHChannel2D</code></a></td>
-<td align="left"><strong>N</strong></td>
-<td align="left"><a href="#shell"><code>Shell</code></a></td>
-<td align="left"><a href="#tableentry"><code>TableEntry</code></a></td>
-<td align="left"></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#diagonalmsg"><code>DiagonalMsg</code></a></td>
-<td align="left"><a href="#hhgate"><code>HHGate</code></a></td>
-<td align="left"><a href="#nernst"><code>Nernst</code></a></td>
-<td align="left"><a href="#simmanager"><code>SimManager</code></a></td>
-<td align="left"><a href="#testsched"><code>testSched</code></a></td>
-<td align="left"></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#diffamp"><code>DiffAmp</code></a></td>
-<td align="left"><a href="#hhgate2d"><code>HHGate2D</code></a></td>
-<td align="left"><a href="#neuromesh"><code>NeuroMesh</code></a></td>
-<td align="left"><a href="#singlemsg"><code>SingleMsg</code></a></td>
-<td align="left"><a href="#tick"><code>Tick</code></a></td>
-<td align="left"></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#diskpanel"><code>DiskPanel</code></a></td>
-<td align="left"><a href="#hsolve"><code>HSolve</code></a></td>
-<td align="left"><a href="#neuron"><code>Neuron</code></a></td>
-<td align="left"><a href="#solverjunction"><code>SolverJunction</code></a></td>
-<td align="left"><a href="#tripanel"><code>TriPanel</code></a></td>
-<td align="left"></td>
-</tr>
-<tr class="odd">
-<td align="left"><strong>E</strong></td>
-<td align="left"><strong>I</strong></td>
-<td align="left"><a href="#neutral"><code>Neutral</code></a></td>
-<td align="left"><a href="#sparsemsg"><code>SparseMsg</code></a></td>
-<td align="left"><strong>V</strong></td>
-<td align="left"></td>
-</tr>
-</tbody>
-</table>
-<h1 id="index-for-moose-functions">Index for MOOSE Functions</h1>
-<table>
-<tbody>
-<tr class="odd">
-<td align="left"><strong>C</strong></td>
-<td align="left"><a href="#element"><code>element</code></a></td>
-<td align="left"><a href="#getmoosedoc"><code>getmoosedoc</code></a></td>
-<td align="left"><a href="#move"><code>move</code></a></td>
-<td align="left"><a href="#savemodel"><code>saveModel</code></a></td>
-<td align="left"><a href="#stop"><code>stop</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#ce"><code>ce</code></a></td>
-<td align="left"><a href="#exists"><code>exists</code></a></td>
-<td align="left"><strong>I</strong></td>
-<td align="left"><strong>P</strong></td>
-<td align="left"><a href="#seed"><code>seed</code></a></td>
-<td align="left"><a href="#syncdatahandler"><code>syncDataHandler</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#connect"><code>connect</code></a></td>
-<td align="left"><strong>G</strong></td>
-<td align="left"><a href="#isrunning"><code>isRunning</code></a></td>
-<td align="left"><a href="#pwe"><code>pwe</code></a></td>
-<td align="left"><a href="#setclock"><code>setClock</code></a></td>
-<td align="left"><strong>U</strong></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#copy"><code>copy</code></a></td>
-<td align="left"><a href="#getcwe"><code>getCwe</code></a></td>
-<td align="left"><strong>L</strong></td>
-<td align="left"><strong>Q</strong></td>
-<td align="left"><a href="#setcwe"><code>setCwe</code></a></td>
-<td align="left"><a href="#useclock"><code>useClock</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><strong>D</strong></td>
-<td align="left"><a href="#getfield"><code>getField</code></a></td>
-<td align="left"><a href="#le"><code>le</code></a></td>
-<td align="left"><a href="#quit"><code>quit</code></a></td>
-<td align="left"><a href="#showfield"><code>showfield</code></a></td>
-<td align="left"><strong>W</strong></td>
-</tr>
-<tr class="even">
-<td align="left"><a href="#delete"><code>delete</code></a></td>
-<td align="left"><a href="#getfielddict"><code>getFieldDict</code></a></td>
-<td align="left"><a href="#listmsg"><code>listmsg</code></a></td>
-<td align="left"><strong>R</strong></td>
-<td align="left"><a href="#showfields"><code>showfields</code></a></td>
-<td align="left"><a href="#wildcardfind"><code>wildcardFind</code></a></td>
-</tr>
-<tr class="odd">
-<td align="left"><a href="#doc"><code>doc</code></a></td>
-<td align="left"><a href="#getfielddoc"><code>getfielddoc</code></a></td>
-<td align="left"><a href="#loadmodel"><code>loadModel</code></a></td>
-<td align="left"><a href="#reinit"><code>reinit</code></a></td>
-<td align="left"><a href="#showmsg"><code>showmsg</code></a></td>
-<td align="left"><a href="#writesbml"><code>writeSBML</code></a></td>
-</tr>
-<tr class="even">
-<td align="left"><strong>E</strong></td>
-<td align="left"><a href="#getfieldnames"><code>getFieldNames</code></a></td>
-<td align="left"><strong>M</strong></td>
-<td align="left"><strong>S</strong></td>
-<td align="left"><a href="#start"><code>start</code></a></td>
-<td align="left"></td>
-</tr>
-</tbody>
-</table>
-<h1 id="moose-classes">MOOSE Classes</h1>
-<h2 id="adaptor">Adaptor</h2>
-<p><strong>Author</strong>: Upinder S. Bhalla, 2008, NCBS</p>
-<p><strong>Description</strong>: Averages and rescales values to couple different kinds of simulation</p>
-<h4 id="value-fields">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>inputOffset</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Offset to apply to input message, before scaling</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputOffset</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Offset to apply at output, after scaling</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>scale</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Scaling factor to apply to input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">This is the linearly transformed output.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputSrc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends the output value every timestep.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestInput</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Sends out the request. Issued from the process call.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>input</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Input message to the adaptor. If multiple inputs are received, the system averages the inputs.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'process' call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'reinit' call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleInput</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handle the returned value.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process message from the scheduler.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>inputRequest</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to request and handle value messages from fields.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="annotator">Annotator</h2>
-<h4 id="value-fields-1">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">x field. Typically display coordinate x</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">y field. Typically display coordinate y</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">z field. Typically display coordinate z</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>notes</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">A string to hold some text notes about parent object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>color</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">A string to hold a text string specifying display color.Can be a regular English color name, or an rgb code rrrgggbbb</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>textColor</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">A string to hold a text string specifying color for text labelthat might be on the display for this object.Can be a regular English color name, or an rgb code rrrgggbbb</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>icon</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">A string to specify icon to use for display</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-1">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-1">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-1">Shared message fields</h4>
-<h4 id="lookup-fields-1">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="arith">Arith</h2>
-<h4 id="value-fields-2">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>function</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Arithmetic function to perform on inputs.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputValue</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Value of output as computed last timestep.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>arg1Value</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Value of arg1 as computed last timestep.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-2">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out the computed value</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-2">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>arg1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles argument 1. This just assigns it</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>arg2</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles argument 2. This just assigns it</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>arg3</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles argument 3. This sums in each input, and clears each clock tick.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>arg1x2</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Store the product of the two arguments in output_</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-2">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-2">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>anyValue</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Value of any of the internal fields, output, arg1, arg2, arg3,as specified by the index argument from 0 to 3.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="boundary">Boundary</h2>
-<h4 id="value-fields-3">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reflectivity</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">What happens to a molecule hitting it: bounces, absorbed, diffused?</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-3">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toAdjacent</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Dummy message going to adjacent compartment.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toInside</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Dummy message going to surrounded compartment.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-3">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>adjacent</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Dummy message coming from adjacent compartment to current oneImplies that compts are peers: do not surround each other</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>outside</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Dummy message coming from surrounding compartment to this one.Implies that the originating compartment surrounds this one</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-3">Shared message fields</h4>
-<h4 id="lookup-fields-3">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="bufpool">BufPool</h2>
-<h4 id="value-fields-4">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-4">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-4">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>increment</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Increments mol numbers by specified amount. Can be +ve or -ve</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>decrement</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Decrements mol numbers by specified amount. Can be +ve or -ve</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-4">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-4">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="caconc">CaConc</h2>
-<h4 id="value-fields-5">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ca</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Calcium concentration.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>CaBasal</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Basal Calcium concentration.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ca_base</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Basal Calcium concentration, synonym for CaBasal</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>tau</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Settling time for Ca concentration</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>B</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Volume scaling factor</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>thick</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Thickness of Ca shell.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ceiling</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>floor</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Floor value for Ca concentration. If Ca < floor, Ca = floor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-5">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>concOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of Ca in pool</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-5">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>current</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Calcium Ion current, due to be converted to conc.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>currentFraction</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Fraction of total Ion current, that is carried by Ca2+.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>increase</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Any input current that increases the concentration.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>decrease</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Any input current that decreases the concentration.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>basal</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Synonym for assignment of basal conc.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-5">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message to receive Process message from scheduler</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-5">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="chanbase">ChanBase</h2>
-<h4 id="value-fields-6">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gbar</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximal channel conductance</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal potential of channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel conductance variable</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current variable</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-6">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>permeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance term going out to GHK object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-6">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-6">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message to Goldman-Hodgkin-Katz object</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-6">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="chemmesh">ChemMesh</h2>
-<h4 id="value-fields-7">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numDimensions</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of spatial dimensions of this compartment. Usually 3 or 2</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-7">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>meshSplit</code></strong></td>
-<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td>
-<td align="left">Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>meshStats</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-7">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>buildDefaultMesh</code></strong></td>
-<td align="left"><code>double,unsigned int</code></td>
-<td align="left">Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleRequestMeshStats</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles request from SimManager for mesh stats</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleNodeInfo</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-7">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>nodeMeshing</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-7">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="cinfo">Cinfo</h2>
-<p><strong>Author</strong>: Upi Bhalla</p>
-<p><strong>Description</strong>: Class information object.</p>
-<h4 id="value-fields-8">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>docs</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Documentation</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>baseClass</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of base class</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-8">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-8">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-8">Shared message fields</h4>
-<h4 id="lookup-fields-8">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="clock">Clock</h2>
-<h4 id="value-fields-9">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>runTime</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Duration to run the simulation</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>currentTime</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current simulation time</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nsteps</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of steps to advance the simulation, in units of the smallest timestep on the clock ticks</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numTicks</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of clock ticks</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>currentStep</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Current simulation step</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>dts</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Utility function returning the dt (timestep) of all ticks.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>isRunning</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Utility function to report if simulation is in progress.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-9">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>childTick</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Parent of Tick element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>finished</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Signal for completion of run</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ack</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">Acknowledgement signal for receipt/completion of function.Goes back to Shell on master node</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-9">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>start</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sets off the simulation for the specified duration</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>step</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Sets off the simulation for the specified # of steps</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>stop</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Halts the simulation, with option to restart seamlessly</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>setupTick</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Sets up a specific clock tick: args tick#, dt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Zeroes out all ticks, starts at t = 0</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-9">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>clockControl</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Controls all scheduling aspects of Clock, usually from Shell</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-9">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="compartment">Compartment</h2>
-<p><strong>Author</strong>: Upi Bhalla</p>
-<p><strong>Description</strong>: Compartment object, for branching neuron models.</p>
-<h4 id="value-fields-10">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">membrane potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Cm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane capacitance</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Em</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Resting membrane potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Im</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current going through membrane</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>inject</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current injection to deliver into compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>initVm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value for membrane potential</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Rm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane resistance</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ra</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Axial resistance of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diameter</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diameter of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>length</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Length of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>x0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">X coordinate of start of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Y coordinate of start of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>z0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Z coordinate of start of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">x coordinate of end of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">y coordinate of end of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">z coordinate of end of compartment</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-10">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>VmOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Vm value of compartment on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>axialOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Vm value of compartment to adjacent compartments,on each timestep</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>raxialOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out Raxial information on each timestep, fields are Ra and Vm</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-10">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>injectMsg</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>randInject</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>injectMsg</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cable</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message for organizing compartments into groups, calledcables. Doesn't do anything.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'process' call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'reinit' call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>initProc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>initReinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles Reinit call for the 'init' phase of the Compartment calculations.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleChannel</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles conductance and Reversal potential arguments from Channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleRaxial</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles Raxial info: arguments are Ra and Vm.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleAxial</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Axial information. Argument is just Vm.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-10">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process messages from the scheduler objects. The Process should be called <em>second</em> in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>init</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>axial</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>raxial</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-10">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="cplxenzbase">CplxEnzBase</h2>
-<p><strong>Author</strong>: Upi Bhalla</p>
-<p><strong>Description</strong>:: Base class for mass-action enzymes in which there is an explicit pool for the enzyme-substrate complex. It models the reaction: E + S <===> E.S ----> E + P</p>
-<h4 id="value-fields-11">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Km</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numKm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in number units, volume dependent</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kcat</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant for enzyme, units 1/sec</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>k1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward reaction from enz + sub to complex</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>k2</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse reaction from complex to enz + sub</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>k3</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant from complex to product + enz</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ratio</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Ratio of k2/k3</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concK1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">K1 expressed in concentration (1/millimolar.sec) units</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-11">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toEnz</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toCplx</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-11">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product. Dummy.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cplxDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of enz-sub complex</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-11">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to product molecule</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enz</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to enzyme pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cplx</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to enz-sub complex pool</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-11">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="cubemesh">CubeMesh</h2>
-<h4 id="value-fields-12">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numDimensions</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of spatial dimensions of this compartment. Usually 3 or 2</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>isToroid</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag. True when the mesh should be toroidal, that is,when going beyond the right face brings us around to theleft-most mesh entry, and so on. If we have nx, ny, nzentries, this rule means that the coordinate (x, ny, z)will map onto (x, 0, z). Similarly,(-1, y, z) -> (nx-1, y, z)Default is false</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>preserveNumEntries</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag. When it is true, the numbers nx, ny, nz remainunchanged when x0, x1, y0, y1, z0, z1 are altered. Thusdx, dy, dz would change instead. When it is false, thendx, dy, dz remain the same and nx, ny, nz are altered.Default is true</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>x0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">X coord of one end</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Y coord of one end</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>z0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Z coord of one end</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">X coord of other end</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Y coord of other end</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Z coord of other end</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>dx</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">X size for mesh</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>dy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Y size for mesh</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>dz</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Z size for mesh</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nx</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of subdivisions in mesh in X</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ny</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of subdivisions in mesh in Y</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nz</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of subdivisions in mesh in Z</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>coords</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Set all the coords of the cuboid at once. Order is:x0 y0 z0 x1 y1 z1 dx dy dz</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>meshToSpace</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array in which each mesh entry stores spatial (cubic) index</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>spaceToMesh</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array in which each space index (obtained by linearizing the xyz coords) specifies which meshIndex is present.In many cases the index will store the EMPTY flag if there isno mesh entry at that spatial location</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>surface</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array specifying surface of arbitrary volume within the CubeMesh. All entries must fall within the cuboid. Each entry of the array is a spatial index obtained by linearizing the ix, iy, iz coordinates within the cuboid. So, each entry == ( iz * ny + iy ) * nx + ixNote that the voxels listed on the surface are WITHIN the volume of the CubeMesh object</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-12">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>meshSplit</code></strong></td>
-<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td>
-<td align="left">Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>meshStats</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-12">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>buildDefaultMesh</code></strong></td>
-<td align="left"><code>double,unsigned int</code></td>
-<td align="left">Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleRequestMeshStats</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles request from SimManager for mesh stats</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleNodeInfo</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-12">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>nodeMeshing</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-12">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="cylmesh">CylMesh</h2>
-<h4 id="value-fields-13">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numDimensions</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of spatial dimensions of this compartment. Usually 3 or 2</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>x0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">x coord of one end</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">y coord of one end</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>z0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">z coord of one end</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>r0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Radius of one end</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>x1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">x coord of other end</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">y coord of other end</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>z1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">z coord of other end</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>r1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Radius of other end</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>lambda</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Length constant to use for subdivisionsThe system will attempt to subdivide using compartments oflength lambda on average. If the cylinder has different enddiameters r0 and r1, it will scale to smaller lengthsfor the smaller diameter end and vice versa.Once the value is set it will recompute lambda as totLength/numEntries</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>coords</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">All the coords as a single vector: x0 y0 z0 x1 y1 z1 r0 r1 lambda</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>totLength</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Total length of cylinder</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-13">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>meshSplit</code></strong></td>
-<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td>
-<td align="left">Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>meshStats</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-13">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>buildDefaultMesh</code></strong></td>
-<td align="left"><code>double,unsigned int</code></td>
-<td align="left">Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleRequestMeshStats</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles request from SimManager for mesh stats</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleNodeInfo</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-13">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>nodeMeshing</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-13">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="cylpanel">CylPanel</h2>
-<h4 id="value-fields-14">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nPts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of points used by panel to specify geometry</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nDims</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Dimensions used by panel to specify geometry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numNeighbors</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Neighbors of panel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>shapeId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Identifier for shape type, as used by Smoldyn</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>coords</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-14">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toNeighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Identifies neighbors of the current panel</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-14">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>neighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles incoming message from neighbor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-14">Shared message fields</h4>
-<h4 id="lookup-fields-14">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">x coordinate identified by index</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">y coordinate identified by index</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">z coordinate identified by index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="diagonalmsg">DiagonalMsg</h2>
-<h4 id="value-fields-15">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>e1</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>e2</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>stride</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">The stride is the increment to the src DataId that gives thedest DataId. It can be positive or negative, but bounds checkingtakes place and it does not wrap around.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-15">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-15">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-15">Shared message fields</h4>
-<h4 id="lookup-fields-15">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="diffamp">DiffAmp</h2>
-<h4 id="value-fields-16">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>gain</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Gain of the amplifier. The output of the amplifier is the difference between the totals in plus and minus inputs multiplied by the gain. Defaults to 1</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>saturation</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Saturation is the bound on the output. If output goes beyond the +/-saturation range, it is truncated to the closer of +saturation and -saturation. Defaults to the maximum double precision floating point number representable on the system.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Output of the amplifier, i.e. gain * (plus - minus).</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-16">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current output level.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-16">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>gainIn</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Destination message to control gain dynamically.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>plusIn</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Positive input terminal of the amplifier. All the messages connected here are summed up to get total positive input.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>minusIn</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Negative input terminal of the amplifier. All the messages connected here are summed up to get total positive input.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call, updates internal time stamp.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-16">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-16">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="diskpanel">DiskPanel</h2>
-<h4 id="value-fields-17">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nPts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of points used by panel to specify geometry</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nDims</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Dimensions used by panel to specify geometry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numNeighbors</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Neighbors of panel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>shapeId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Identifier for shape type, as used by Smoldyn</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>coords</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-17">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toNeighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Identifies neighbors of the current panel</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-17">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>neighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles incoming message from neighbor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-17">Shared message fields</h4>
-<h4 id="lookup-fields-17">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">x coordinate identified by index</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">y coordinate identified by index</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">z coordinate identified by index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="enz">Enz</h2>
-<h4 id="value-fields-18">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Km</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numKm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in number units, volume dependent</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kcat</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant for enzyme, units 1/sec</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>k1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward reaction from enz + sub to complex</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>k2</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse reaction from complex to enz + sub</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>k3</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant from complex to product + enz</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ratio</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Ratio of k2/k3</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concK1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">K1 expressed in concentration (1/millimolar.sec) units</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-18">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toEnz</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toCplx</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-18">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product. Dummy.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cplxDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of enz-sub complex</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-18">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to product molecule</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enz</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to enzyme pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cplx</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to enz-sub complex pool</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-18">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="enzbase">EnzBase</h2>
-<h4 id="value-fields-19">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Km</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numKm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in number units, volume dependent</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kcat</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant for enzyme, units 1/sec</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-19">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-19">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product. Dummy.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-19">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to product molecule</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-19">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="finfo">Finfo</h2>
-<h4 id="value-fields-20">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of Finfo</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>docs</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Documentation for Finfo</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>type</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">RTTI type info for this Finfo</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>src</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Subsidiary SrcFinfos. Useful for SharedFinfos</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>dest</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Subsidiary DestFinfos. Useful for SharedFinfos</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-20">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-20">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-20">Shared message fields</h4>
-<h4 id="lookup-fields-20">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="funcbase">FuncBase</h2>
-<h4 id="value-fields-21">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>result</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Outcome of function computation</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-21">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out sum on each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-21">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>input</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-21">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-21">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="funcpool">FuncPool</h2>
-<h4 id="value-fields-22">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-22">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-22">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>increment</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Increments mol numbers by specified amount. Can be +ve or -ve</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>decrement</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Decrements mol numbers by specified amount. Can be +ve or -ve</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>input</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles input to control value of n_</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-22">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-22">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="ghk">GHK</h2>
-<h4 id="value-fields-23">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane current</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal Potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>T</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Temperature of system</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>p</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Permeability of channel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane potential</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Cin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Internal concentration</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Cout</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">External ion concentration</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>valency</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Valence of ion</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-23">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>VmOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Relay of membrane potential Vm.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">MembraneCurrent.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-23">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleVm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>addPermeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles permeability message coming in from channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>CinDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Alias for set_Cin</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>CoutDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Alias for set_Cout</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>addPermeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles permeability message coming in from channel</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-23">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message from channel to current Goldman-Hodgkin-Katz objectThis shared message connects to an HHChannel. The first entry is a MsgSrc which relays the Vm received from a compartment. The second entry is a MsgDest which receives channel conductance, and interprets it as permeability.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-23">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="geometry">Geometry</h2>
-<h4 id="value-fields-24">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>epsilon</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">epsilon is the max deviation of surface-point from surface.I think it refers to when the molecule is stuck to the surface. Need to check with Steven.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>neighdist</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">neighdist is capture distance from one panel to another.When a molecule diffuses off one panel and is within neighdist of the other, it is captured by the second.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-24">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>returnSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Return size of compartment</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-24">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleSizeRequest</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles a request for size. Part of SharedMsg to ChemCompt.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-24">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>compt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to compartment(s) to specify geometry.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-24">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="group">Group</h2>
-<h4 id="value-fields-25">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-25">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-25">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-25">Shared message fields</h4>
-<h4 id="lookup-fields-25">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="gslintegrator">GslIntegrator</h2>
-<h4 id="value-fields-26">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>isInitialized</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">True if the Stoich message has come in to set parms</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>method</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Numerical method to use.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>relativeAccuracy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Accuracy criterion</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>absoluteAccuracy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Another accuracy criterion</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-26">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-26">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>stoich</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Handle data from Stoich</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-26">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-26">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="gslstoich">GslStoich</h2>
-<h4 id="value-fields-27">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>isInitialized</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">True if the Stoich message has come in to set parms</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>method</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Numerical method to use.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>relativeAccuracy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Accuracy criterion</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>absoluteAccuracy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Another accuracy criterion</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>compartment</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">This is the Id of the compartment, which must be derived fromthe ChemMesh baseclass. The GslStoich needsthe ChemMesh Id only for diffusion, and one can pass in Id() instead if there is no diffusion, or just leave it unset.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-27">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-27">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>addJunction</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Add a junction between the current solver and the one whose Id is passed in.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>dropJunction</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Drops a junction between the current solver and the one whose Id is passed in. Ignores if no junction.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>stoich</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Assign the StoichCore and ChemMesh Ids. The GslStoich needsthe StoichCore pointer in all cases, in order to perform allcalculations.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>initProc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles init call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>initReinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles initReinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-27">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>init</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for init and initReinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-27">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="gssastoich">GssaStoich</h2>
-<p><strong>Author</strong>: Upinder S. Bhalla, 2008, 2011, NCBS</p>
-<p><strong>Description</strong>: GssaStoich: Gillespie Stochastic Simulation Algorithm object.Closely based on the Stoich object and inherits its handling functions for constructing the matrix. Sets up stoichiometry matrix based calculations from a</p>
-<p>wildcard path for the reaction system.Knows how to compute derivatives for most common things, also knows how to handle special cases where the object will have to do its own computation.Generates a stoichiometry matrix, which is useful for lots of other operations as well.</p>
-<h4 id="value-fields-28">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>useOneWayReacs</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nVarPools</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of variable molecule pools in the reac system</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numMeshEntries</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of meshEntries in reac-diff system</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>estimatedDt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Path of reaction system to take over</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Path of reaction system to take over and solve</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>method</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Numerical method to use for the GssaStoich. The defaultand currently the only method is Gillespie1.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-28">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>plugin</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Sends out Stoich Id so that plugins can directly access fields and functions</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nodeDiffBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Sends mol #s across boundary between nodes, to calculate diffusionterms. arg1 is originating node, arg2 is list of meshIndices forwhich data is being transferred, and arg3 are the 'n' values forall the pools on the specified meshIndices, to be plugged intothe appropriate place on the recipient node's S_ matrix</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>poolsReactingAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">A vector of mol counts (n) of those pools that react across a boundary. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacRollbacksAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">Occasionally, a Gillespie advance will cause the mol conc on the target stoich side to become negative. If so, this message does a patch up job by telling the originating Stoich to roll back to the specified number of reac firings, which is the max that the target was able to handle. This is probably numerically naughty, but it is better than negative concentrations</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reacRatesAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">A vector of reac rates (V) of each reaction crossing the boundary between compartments. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. In the case of Gillespie calculations <em>V</em> is the integer # of transitions (firings) of each reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-28">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>meshSplit</code></strong></td>
-<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td>
-<td align="left">Handles message from ChemMesh that defines how meshEntries are decomposed on this node, and how they communicate between nodes.Args: (oldVol, volumeVectorForAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#])</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleReacRatesAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handlePoolsReactingAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of pool #s for every pool that reacts across the boundary, in every mesh entry. that reacts across a boundary, in every mesh entry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleReacRollbacksAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. Only one side does the calculations to assure mass conservation. There are rare cases when the calculations of one solver, typically a Gillespie one, gives such a large change that the concentrations on the other side would become negative in one or more molecules This message handles such cases on the Gillespie side, by telling the solver to roll back its recent calculation and instead use the specified vector for the rates, that is the # of mols changed in the latest timestep. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinint call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-28">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>boundaryReacOut</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>boundaryReacIn</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-28">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="hdf5datawriter">HDF5DataWriter</h2>
-<p><strong>Author</strong>: Subhasis Ray</p>
-<p><strong>Description</strong>: HDF5 file writer for saving data tables. It saves the tables connected to it via <code>requestData</code> field into an HDF5 file. The path of the table is maintained in the HDF5 file, with a HDF5 group for each element above the table.</p>
-<p>Thus, if you have a table <code>/data/VmTable</code> in MOOSE, then it will be written as an HDF5 table called <code>VmTable</code> inside an HDF5 Group called <code>data</code>.</p>
-<p>However Table inside Table is considered a pathological case and is not handled.</p>
-<p>At every process call it writes the contents of the tables to the file and clears the table vectors. You can explicitly force writing of the data via the <code>flush</code> function.</p>
-<h4 id="value-fields-29">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>filename</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of the file associated with this HDF5 writer object.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>isOpen</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">True if this object has an open file handle.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>mode</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Depending on mode, if file already exists, if mode=1, data will be appended to existing file, if mode=2, file will be truncated, if mode=4, no writing will happen.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-29">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestData</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Sends request for a field to target object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>clear</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Send request to clear a Table vector.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-29">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>flush</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Write all buffer contents to file and clear the buffers.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>recvData</code></strong></td>
-<td align="left"><code>bad</code></td>
-<td align="left">Handles data sent back following request</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle process calls. Write data to file and clear all Table objects associated with this. Hence you want to keep it on a slow clock 1000 times or more slower than that for the tables.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Reinitialize the object. If the current file handle is valid, it tries to close that and open the file specified in current filename field.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-29">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message to receive process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-29">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="hdf5writerbase">HDF5WriterBase</h2>
-<p><strong>Author</strong>: Subhasis Ray</p>
-<p><strong>Description</strong>: HDF5 file writer base class. This is not to be used directly. Instead, it should be subclassed to provide specific data writing functions. This class provides most basic properties like filename, file opening mode, file open status.</p>
-<h4 id="value-fields-30">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>filename</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of the file associated with this HDF5 writer object.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>isOpen</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">True if this object has an open file handle.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>mode</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Depending on mode, if file already exists, if mode=1, data will be appended to existing file, if mode=2, file will be truncated, if mode=4, no writing will happen.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-30">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-30">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>flush</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Write all buffer contents to file and clear the buffers.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-30">Shared message fields</h4>
-<h4 id="lookup-fields-30">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="hhchannel">HHChannel</h2>
-<h4 id="value-fields-31">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gbar</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximal channel conductance</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal potential of channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel conductance variable</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current variable</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Xpower</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Power for X gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ypower</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Power for Y gate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Zpower</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Power for Z gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>instant</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>X</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">State variable for X gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Y</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">State variable for Y gate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Z</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">State variable for Y gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>useConcentration</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Flag: when true, use concentration message rather than Vm tocontrol Z gate</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-31">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>permeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance term going out to GHK object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-31">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>concen</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Incoming message from Concen object to specific conc to usein the Z gate calculations</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>createGate</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Function to create specified gate.Argument: Gate type [X Y Z]</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-31">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message to Goldman-Hodgkin-Katz object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</td>
-</tr>
-<tr class="even">
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-31">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="hhchannel2d">HHChannel2D</h2>
-<h4 id="value-fields-32">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gbar</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximal channel conductance</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal potential of channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel conductance variable</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current variable</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Xindex</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">String for setting X index.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Yindex</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">String for setting Y index.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Zindex</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">String for setting Z index.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Xpower</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Power for X gate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ypower</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Power for Y gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Zpower</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Power for Z gate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>instant</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>X</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">State variable for X gate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Y</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">State variable for Y gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Z</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">State variable for Y gate</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-32">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>permeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance term going out to GHK object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-32">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>concen</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Incoming message from Concen object to specific conc to useas the first concen variable</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concen2</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Incoming message from Concen object to specific conc to useas the second concen variable</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-32">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message to Goldman-Hodgkin-Katz object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</td>
-</tr>
-<tr class="even">
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-32">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="hhgate">HHGate</h2>
-<h4 id="value-fields-33">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>alpha</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Parameters for voltage-dependent rates, alpha:Set up alpha term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>beta</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Parameters for voltage-dependent rates, beta:Set up beta term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>tau</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Parameters for voltage-dependent rates, tau:Set up tau curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mInfinity</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Parameters for voltage-dependent rates, mInfinity:Set up mInfinity curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>min</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum range for lookup</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>max</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum range for lookup</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>divs</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Divisions for lookup. Zero means to use linear interpolation</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>tableA</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Table of A entries</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>tableB</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Table of alpha + beta entries</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>useInterpolation</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag: use linear interpolation if true, else direct lookup</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-33">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-33">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>setupAlpha</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>setupTau</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Identical to setupAlpha, except that the forms specified bythe 13 parameters are for the tau and m-infinity curves ratherthan the alpha and beta terms. So the parameters are:setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmaxAs before, the equation describing each curve is:y(x) = (A + B * x) / (C + exp((x + D) / F))</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>tweakAlpha</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Dummy function for backward compatibility. It used to convertthe tables from alpha, beta values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>tweakTau</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Dummy function for backward compatibility. It used to convertthe tables from tau, minf values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>setupGate</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Sets up one gate at a time using the alpha/beta form.Has 9 parameters, as follows:setupGate A B C D F xdivs xmin xmax is_betaThis sets up the gate using the equation:y(x) = (A + B * x) / (C + exp((x + D) / F))Deprecated.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-33">Shared message fields</h4>
-<h4 id="lookup-fields-33">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>A</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">lookupA: Look up the A gate value from a double. Usually doesso by direct scaling and offset to an integer lookup, usinga fine enough table granularity that there is little error.Alternatively uses linear interpolation.The range of the double is predefined based on knowledge ofvoltage or conc ranges, and the granularity is specified bythe xmin, xmax, and dV fields.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>B</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">lookupB: Look up the B gate value from a double.Note that this looks up the raw tables, which are transformedfrom the reference parameters.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="hhgate2d">HHGate2D</h2>
-<h4 id="value-fields-34">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-34">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-34">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-34">Shared message fields</h4>
-<h4 id="lookup-fields-34">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>A</code></strong></td>
-<td align="left"><code>vector<double>,double</code></td>
-<td align="left">lookupA: Look up the A gate value from two doubles, passedin as a vector. Uses linear interpolation in the 2D tableThe range of the lookup doubles is predefined based on knowledge of voltage or conc ranges, and the granularity is specified by the xmin, xmax, and dx field, and their y-axis counterparts.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>B</code></strong></td>
-<td align="left"><code>vector<double>,double</code></td>
-<td align="left">lookupB: Look up B gate value from two doubles in a vector.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="hsolve">HSolve</h2>
-<h4 id="value-fields-35">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>seed</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Use this field to specify path to a 'seed' compartment, that is, any compartment within a neuron. The HSolve object uses this seed as a handle to discover the rest of the neuronal model, which means all the remaining compartments, channels, synapses, etc.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>target</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Specifies the path to a compartmental model to be taken over. This can be the path to any container object that has the model under it (found by performing a deep search). Alternatively, this can also be the path to any compartment within the neuron. This compartment will be used as a handle to discover the rest of the model, which means all the remaining compartments, channels, synapses, etc.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>dt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The time-step for this solver.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>caAdvance</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">This flag determines how current flowing into a calcium pool is computed. A value of 0 means that the membrane potential at the beginning of the time-step is used for the calculation. This is how GENESIS does its computations. A value of 1 means the membrane potential at the middle of the time-step is used. This is the correct way of integration, and is the default way.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>vDiv</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Specifies number of divisions for lookup tables of voltage-sensitive channels.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>vMin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Specifies the lower bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>vMax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Specifies the upper bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>caDiv</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Specifies number of divisions for lookup tables of calcium-sensitive channels.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>caMin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Specifies the lower bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>caMax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Specifies the upper bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-35">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-35">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'process' call: Solver advances by one time-step.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'reinit' call: Solver reads in model.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-35">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'reinit' and 'process' calls from a clock.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-35">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="hemispherepanel">HemispherePanel</h2>
-<h4 id="value-fields-36">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nPts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of points used by panel to specify geometry</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nDims</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Dimensions used by panel to specify geometry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numNeighbors</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Neighbors of panel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>shapeId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Identifier for shape type, as used by Smoldyn</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>coords</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-36">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toNeighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Identifies neighbors of the current panel</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-36">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>neighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles incoming message from neighbor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-36">Shared message fields</h4>
-<h4 id="lookup-fields-36">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">x coordinate identified by index</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">y coordinate identified by index</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">z coordinate identified by index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="intfire">IntFire</h2>
-<h4 id="value-fields-37">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numSynapses</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of synapses on SynBase</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane potential</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>tau</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">charging time-course</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>thresh</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">firing threshold</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>refractoryPeriod</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum time between successive spikes</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-37">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>spike</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out spike events</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-37">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-37">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-37">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="interpol2d">Interpol2D</h2>
-<h4 id="value-fields-38">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>xmin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum value for x axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>xmax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximum value for x axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>xdivs</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of divisions on x axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>dx</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Increment on x axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ymin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum value for y axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ymax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximum value for y axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ydivs</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of divisions on y axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>dy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Increment on y axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>tableVector2D</code></strong></td>
-<td align="left"><code>vector< vector<double> ></code></td>
-<td align="left">Get the entire table.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-38">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>trig</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">respond to a request for a value lookup</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-38">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lookup</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Looks up table value based on indices v1 and v2, and sendsvalue back using the 'trig' message</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-38">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>lookupReturn2D</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message for doing lookups on the table. Receives 2 doubles: x, y. Sends back a double with the looked-up z value.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-38">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>table</code></strong></td>
-<td align="left"><code>vector<unsigned int>,double</code></td>
-<td align="left">Lookup an entry on the table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>vector<double>,double</code></td>
-<td align="left">Interpolated value for specified x and y. This is provided for debugging. Normally other objects will retrieve interpolated values via lookup message.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="izhikevichnrn">IzhikevichNrn</h2>
-<h4 id="value-fields-39">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vmax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximum membrane potential. Membrane potential is reset to c whenever it reaches Vmax. NOTE: Izhikevich model specifies the PEAK voltage, rather than THRSHOLD voltage. The threshold depends on the previous history.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>c</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reset potential. Membrane potential is reset to c whenever it reaches Vmax.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>d</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Parameter d in Izhikevich model. Unit is V/s.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>a</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Parameter a in Izhikevich model. Unit is s^{-1}</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>b</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Parameter b in Izhikevich model. Unit is s^{-1}</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>u</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Parameter u in Izhikevich equation. Unit is V/s</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane potential, equivalent to v in Izhikevich equation.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Im</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Total current going through the membrane. Unit is A.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Rm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Hidden cefficient of input current term (I) in Izhikevich model. Defaults to 1e6 Ohm.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>initVm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial membrane potential. Unit is V.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>initU</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of u.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>alpha</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Coefficient of v^2 in Izhikevich equation. Defaults to 0.04 in physiological unit. In SI it should be 40000.0. Unit is V^-1 s^{-1}</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>beta</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Coefficient of v in Izhikevich model. Defaults to 5 in physiological unit, 5000.0 for SI units. Unit is s^{-1}</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>gamma</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Constant term in Izhikevich model. Defaults to 140 in both physiological and SI units. unit is V/s.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-39">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>VmOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Vm</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>spike</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out spike events</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-39">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>injectDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Injection current into the neuron.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Destination message to modify parameter c at runtime.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>dDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Destination message to modify parameter d at runtime.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>bDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Destination message to modify parameter b at runtime</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>aDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Destination message modify parameter a at runtime.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-39">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message to receive Process message from scheduler</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-39">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="leakyiaf">LeakyIaF</h2>
-<h4 id="value-fields-40">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Cm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane capacitance.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Rm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane resistance, inverse of leak-conductance.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Em</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Leak reversal potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane potential</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>initVm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Inital value of membrane potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vreset</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reset potnetial after firing.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vthreshold</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">firing threshold</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>refractoryPeriod</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum time between successive spikes</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>inject</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Injection current.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>tSpike</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Time of the last spike</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-40">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>spike</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out spike events</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>VmOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Vm</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-40">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>injectDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Destination for current input.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-40">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-40">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="mmenz">MMenz</h2>
-<h4 id="value-fields-41">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Km</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numKm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in number units, volume dependent</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kcat</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant for enzyme, units 1/sec</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-41">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-41">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product. Dummy.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-41">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to product molecule</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-41">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="markovchannel">MarkovChannel</h2>
-<h4 id="value-fields-42">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gbar</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximal channel conductance</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal potential of channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel conductance variable</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current variable</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ligandconc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Ligand concentration.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane voltage.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numstates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">The number of states that the channel can occupy.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numopenstates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">The number of states which are open/conducting.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>state</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">This is a row vector that contains the probabilities of finding the channel in each state.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>initialstate</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">This is a row vector that contains the probabilities of finding the channel in each state at t = 0. The state of the channel is reset to this value during a call to reinit()</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>labels</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Labels for each state.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>gbar</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">A row vector containing the conductance associated with each of the open/conducting states.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-42">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>permeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance term going out to GHK object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-42">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleligandconc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Deals with incoming messages containing information of ligand concentration</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handlestate</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Deals with incoming message from MarkovSolver object containing state information of the channel.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-42">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message to Goldman-Hodgkin-Katz object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-42">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="markovgslsolver">MarkovGslSolver</h2>
-<h4 id="value-fields-43">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>isInitialized</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">True if the message has come in to set solver parameters.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>method</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Numerical method to use.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>relativeAccuracy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Accuracy criterion</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>absoluteAccuracy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Another accuracy criterion</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>internalDt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">internal timestep to use.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-43">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>stateOut</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Sends updated state to the MarkovChannel class.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-43">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>init</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Initialize solver parameters.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleQ</code></strong></td>
-<td align="left"><code>vector< vector<double> ></code></td>
-<td align="left">Handles information regarding the instantaneous rate matrix from the MarkovRateTable class.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-43">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-43">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="markovratetable">MarkovRateTable</h2>
-<h4 id="value-fields-44">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane voltage.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ligandconc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Ligand concentration.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Q</code></strong></td>
-<td align="left"><code>vector< vector<double> ></code></td>
-<td align="left">Instantaneous rate matrix.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Dimension of the families of lookup tables. Is always equal to the number of states in the model.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-44">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>instratesOut</code></strong></td>
-<td align="left"><code>vector< vector<double> ></code></td>
-<td align="left">Sends out instantaneous rate information of varying transition rates at each time step.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-44">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleVm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles incoming message containing voltage information.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>init</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Initialization of the class. Allocates memory for all the tables.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleLigandConc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles incoming message containing ligand concentration.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>set1d</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int,Id,unsigned int</code></td>
-<td align="left">Setting up of 1D lookup table for the (i,j)'th rate.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>set2d</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int,Id</code></td>
-<td align="left">Setting up of 2D lookup table for the (i,j)'th rate.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>setconst</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int,double</code></td>
-<td align="left">Setting a constant value for the (i,j)'th rate. Internally, this is stored as a 1-D rate with a lookup table containing 1 entry.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-44">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This message couples the rate table to the compartment. The rate table needs updates on voltage in order to compute the rate table.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-44">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="markovsolver">MarkovSolver</h2>
-<h4 id="value-fields-45">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Q</code></strong></td>
-<td align="left"><code>vector< vector<double> ></code></td>
-<td align="left">Instantaneous rate matrix.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>state</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Current state of the channel.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>initialstate</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Initial state of the channel.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>xmin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum value for x axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>xmax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximum value for x axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>xdivs</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of divisions on x axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>invdx</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reciprocal of increment on x axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ymin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum value for y axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ymax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximum value for y axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ydivs</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of divisions on y axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>invdy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reciprocal of increment on y axis of lookup table</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-45">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>stateOut</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Sends updated state to the MarkovChannel class.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-45">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleVm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles incoming message containing voltage information.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ligandconc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles incoming message containing ligand concentration.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>init</code></strong></td>
-<td align="left"><code>Id,double</code></td>
-<td align="left">Setups the table of matrix exponentials associated with the solver object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-45">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-45">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="markovsolverbase">MarkovSolverBase</h2>
-<h4 id="value-fields-46">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Q</code></strong></td>
-<td align="left"><code>vector< vector<double> ></code></td>
-<td align="left">Instantaneous rate matrix.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>state</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Current state of the channel.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>initialstate</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Initial state of the channel.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>xmin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum value for x axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>xmax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximum value for x axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>xdivs</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of divisions on x axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>invdx</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reciprocal of increment on x axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ymin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum value for y axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ymax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximum value for y axis of lookup table</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ydivs</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of divisions on y axis of lookup table</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>invdy</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reciprocal of increment on y axis of lookup table</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-46">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>stateOut</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Sends updated state to the MarkovChannel class.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-46">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleVm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles incoming message containing voltage information.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ligandconc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles incoming message containing ligand concentration.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>init</code></strong></td>
-<td align="left"><code>Id,double</code></td>
-<td align="left">Setups the table of matrix exponentials associated with the solver object.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-46">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-46">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="mathfunc">MathFunc</h2>
-<h4 id="value-fields-47">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>mathML</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">MathML version of expression to compute</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>function</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">function is for functions of form f(x, y) = x + y</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>result</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">result value</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-47">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out result of computation</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-47">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>arg1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handle arg1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>arg2</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handle arg2</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>arg3</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handle arg3</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>arg4</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handle arg4</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-47">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-47">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="mdouble">Mdouble</h2>
-<h4 id="value-fields-48">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Access function for entire Mdouble object.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>value</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Access function for value field of Mdouble object,which happens also to be the entire contents of the object.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-48">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-48">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-48">Shared message fields</h4>
-<h4 id="lookup-fields-48">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="meshentry">MeshEntry</h2>
-<h4 id="value-fields-49">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Volume of this MeshEntry</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>dimensions</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">number of dimensions of this MeshEntry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>meshType</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder 3. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Coordinates</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Coordinates that define current MeshEntry. Depend on MeshType.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>neighbors</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Indices of other MeshEntries that this one connects to</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>DiffusionArea</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Diffusion area for geometry of interface</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>DiffusionScaling</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Diffusion scaling for geometry of interface</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-49">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Tells the target pool or other entity that the compartment subdivision(meshing) has changed, and that it has to redo its volume and memory allocation accordingly.Arguments are: oldvol, numTotalEntries, startEntry, localIndices, volsThe vols specifies volumes of each local mesh entry. It also specifieshow many meshEntries are present on the local node.The localIndices vector is used for general load balancing only.It has a list of the all meshEntries on current node.If it is empty, we assume block load balancing. In this secondcase the contents of the current node go from startEntry to startEntry + vols.size().</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remeshReacs</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells connected enz or reac that the compartment subdivision(meshing) has changed, and that it has to redo its volume-dependent rate terms like numKf_ accordingly.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-49">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-49">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for updating mesh volumes and subdivisions,typically controls pool sizes</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-49">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="mgblock">MgBlock</h2>
-<h4 id="value-fields-50">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gbar</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximal channel conductance</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal potential of channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel conductance variable</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current variable</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>KMg_A</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">1/eta</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>KMg_B</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">1/gamma</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>CMg</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">[Mg] in mM</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current through MgBlock</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Zk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Charge on ion</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-50">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>permeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance term going out to GHK object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-50">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>origChannel</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left"></td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-50">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message to Goldman-Hodgkin-Katz object</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-50">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="msg">Msg</h2>
-<h4 id="value-fields-51">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>e1</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>e2</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-51">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-51">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-51">Shared message fields</h4>
-<h4 id="lookup-fields-51">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="mstring">Mstring</h2>
-<h4 id="value-fields-52">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Access function for entire Mstring object.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>value</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Access function for value field of Mstring object,which happens also to be the entire contents of the object.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-52">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-52">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-52">Shared message fields</h4>
-<h4 id="lookup-fields-52">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="nmdachan">NMDAChan</h2>
-<p><strong>Author</strong>: Subhasis Ray, 2010, NCBS</p>
-<p><strong>Description</strong>: NMDAChan: Extracellular [Mg2+] dependent NMDA channel.This channel has four states as described by Jahr and Stevens (J. Neurosci. 1990, 10(9)) This implementation is based on equation 4(a) in that article. The channel conductance is defined as : k * g(V, [Mg2+]o) * S(t) where k is a scaling constant. S(t) is the legand gated component of the conductance. It rises linearly for t = tau2. Then decays exponentially with time constant t = tau1. g is a function of voltage and the extracellular [Mg2+] defined as: 1 / { 1 + (a1 + a2) * (a1 * B1 + a2 * B2)/ [A * a1 * (b1 + B1) + A * a2 * (b2 + B2)]}</p>
-<p>a1 = 1e3 * exp( - c0 * V - c1) s^{-1}, c0 = 16.0 / V, c1 = 2.91</p>
-<p>a2 = 1e-3 * [Mg2+] * exp( -c2 * V - c3) mM^{-1} s, c2 = 45.0 / V, c3 = 6.97</p>
-<p>b1 = 1e3 * exp(c4 * V + c5) s^{-1}, c4 = 9.0 / V, c5 = 1.22</p>
-<p>b2 = 1e3 * exp(c6 * V + c7) s^{-1}, c6 = 17.0 / V, c7 = 0.96</p>
-<p>A = 1e3 * exp(-c8) s^{-1}, c8 = 2.847</p>
-<p>B1 = 1e3 * exp(-c9) s^{-1}, c9 = 0.693 s^{-1}</p>
-<p>B2 = 1e3 * exp(-c10) s^{-1}, c10 = 3.101.</p>
-<p>The behaviour of S(t) is as follows:</p>
-<p>If a spike arrives, then the slope of the linear rise of S(t) is incremented by weight / tau2.</p>
-<p>After tau2 time, this component is removed from the slope (reduced by weight/tau) and added over to the rate of decay of S(t).</p>
-<h4 id="value-fields-53">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numSynapses</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of synapses on SynBase</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Gbar</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximal channel conductance</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal potential of channel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel conductance variable</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current variable</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>tau1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Decay time constant for the synaptic conductance, tau1 >= tau2.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>tau2</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Rise time constant for the synaptic conductance, tau1 >= tau2.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>normalizeWeights</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>unblocked</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Fraction of channels recovered from Mg2+ block. This is an intermediate variable which corresponds to g(V, [Mg2+]o) in the equation for conductance: k * g(V, [Mg2+]o) * S(t) where k is a constant.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>MgConc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">External Mg2+ concentration</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>unblocked</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Fraction of channels recovered from Mg2+ block. This is an intermediate variable which corresponds to g(V, [Mg2+]o) in the equation for conductance: k * g(V, [Mg2+]o) * S(t) where k is a constant.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>saturation</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Upper limit on the NMDA conductance.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-53">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>permeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance term going out to GHK object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-53">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>activation</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sometimes we want to continuously activate the channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>modulator</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Modulate channel response</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>MgConcDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Update [Mg2+] from other sources at every time step.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-53">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message to Goldman-Hodgkin-Katz object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message to receive Process message from scheduler</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-53">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>c</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Transition parameters c0 to c10 in the Mg2+ dependentstate transitions.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="nernst">Nernst</h2>
-<h4 id="value-fields-54">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>E</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Computed reversal potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Temperature</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Temperature of cell</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>valence</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Valence of ion in Nernst calculation</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Cin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Internal conc of ion</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Cout</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">External conc of ion</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>scale</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Voltage scale factor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-54">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Eout</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Computed reversal potential</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-54">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ci</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Set internal conc of ion, and immediately send out the updated E</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>co</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Set external conc of ion, and immediately send out the updated E</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-54">Shared message fields</h4>
-<h4 id="lookup-fields-54">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="neuromesh">NeuroMesh</h2>
-<h4 id="value-fields-55">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numDimensions</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of spatial dimensions of this compartment. Usually 3 or 2</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cell</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id for base element of cell model. Uses this to traverse theentire tree of the cell to build the mesh.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>subTree</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">Set of compartments to model. If they happen to be contiguousthen also set up diffusion between the compartments. Can alsohandle cases where the same cell is divided into multiplenon-diffusively-coupled compartments</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>skipSpines</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag: when skipSpines is true, the traversal does not includeany compartment with the string 'spine' or 'neck' in its name,and also then skips compartments below this skipped one.Allows to set up separate mesh for spines, based on the same cell model.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numSegments</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of cylindrical/spherical segments in model</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numDiffCompts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of diffusive compartments in model</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>diffLength</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusive length constant to use for subdivisions. The system willattempt to subdivide cell using diffusive compartments ofthe specified diffusion lengths as a maximum.In order to get integral numbersof compartments in each segment, it may subdivide more finely.Uses default of 0.5 microns, that is, half typical lambda.For default, consider a tau of about 1 second for mostreactions, and a diffusion const of about 1e-12 um^2/sec.This gives lambda of 1 micron</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>geometryPolicy</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Policy for how to interpret electrical model geometry (which is a branching 1-dimensional tree) in terms of 3-D constructslike spheres, cylinders, and cones.There are three options, default, trousers, and cylinder:default mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites and dendrites emerging from soma, proximal diameter is from compt dia. Don't worry about overlap. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.trousers mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites, use a trouser function. Avoid overlap. - For soma, use some variant of trousers. Here we must avoid overlap - For spines, use a way to smoothly merge into parent dend. Radius of curvature should be similar to that of the spine neck. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.cylinder mode: - Use cylinders. Diameter is just compartment dia. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle. - Ignore spatial overlap.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-55">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>meshSplit</code></strong></td>
-<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td>
-<td align="left">Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>meshStats</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-55">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>buildDefaultMesh</code></strong></td>
-<td align="left"><code>double,unsigned int</code></td>
-<td align="left">Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleRequestMeshStats</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles request from SimManager for mesh stats</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleNodeInfo</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>setCellPortion</code></strong></td>
-<td align="left"><code>Id,vector<Id></code></td>
-<td align="left">Tells NeuroMesh to mesh up a subpart of a cell. For nowassumed contiguous.The first argument is the cell Id. The second is the vectorof Ids to consider in meshing up the subpart.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-55">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>nodeMeshing</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-55">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="neuron">Neuron</h2>
-<p><strong>Author</strong>: C H Chaitanya</p>
-<p><strong>Description</strong>: Neuron - A compartment container</p>
-<h4 id="value-fields-56">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-56">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-56">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-56">Shared message fields</h4>
-<h4 id="lookup-fields-56">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="neutral">Neutral</h2>
-<p><strong>Author</strong>: Upinder S. Bhalla, 2007, NCBS</p>
-<p><strong>Description</strong>: Neutral: Base class for all MOOSE classes. Providesaccess functions for housekeeping fields and operations, messagetraversal, and so on.</p>
-<h4 id="value-fields-57">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-57">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-57">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-57">Shared message fields</h4>
-<h4 id="lookup-fields-57">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="onetoallmsg">OneToAllMsg</h2>
-<h4 id="value-fields-58">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>e1</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>e2</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>i1</code></strong></td>
-<td align="left"><code>DataId</code></td>
-<td align="left">DataId of source Element.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-58">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-58">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-58">Shared message fields</h4>
-<h4 id="lookup-fields-58">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="onetoonemsg">OneToOneMsg</h2>
-<h4 id="value-fields-59">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>e1</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>e2</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-59">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-59">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-59">Shared message fields</h4>
-<h4 id="lookup-fields-59">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="pidcontroller">PIDController</h2>
-<h4 id="value-fields-60">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>gain</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">This is the proportional gain (Kp). This tuning parameter scales the proportional term. Larger gain usually results in faster response, but too much will lead to instability and oscillation.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>saturation</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Bound on the permissible range of output. Defaults to maximum double value.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>command</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The command (desired) value of the sensed parameter. In control theory this is commonly known as setpoint(SP).</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>sensed</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sensed (measured) value. This is commonly known as process variable(PV) in control theory.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>tauI</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The integration time constant, typically = dt. This is actually proportional gain divided by integral gain (Kp/Ki)). Larger Ki (smaller tauI) usually leads to fast elimination of steady state errors at the cost of larger overshoot.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>tauD</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The differentiation time constant, typically = dt / 4. This is derivative gain (Kd) times proportional gain (Kp). Larger Kd (tauD) decreases overshoot at the cost of slowing down transient response and may lead to instability.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Output of the PIDController. This is given by: gain * ( error + INTEGRAL[ error dt ] / tau_i + tau_d * d(error)/dt )</td>
-</tr>
-<tr class="even">
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">Where gain = proportional gain (Kp), tau_i = integral gain (Kp/Ki) and tau_d = derivative gain (Kd/Kp). In control theory this is also known as the manipulated variable (MV)</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>error</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The error term, which is the difference between command and sensed value.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>integral</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The integral term. It is calculated as INTEGRAL(error dt) = previous_integral + dt * (error + e_previous)/2.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>derivative</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The derivative term. This is (error - e_previous)/dt.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>e_previous</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The error term for previous step.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-60">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends the output of the PIDController. This is known as manipulated variable (MV) in control theory. This should be fed into the process which we are trying to control.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-60">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>commandIn</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Command (desired value) input. This is known as setpoint (SP) in control theory.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>sensedIn</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sensed parameter - this is the one to be tuned. This is known as process variable (PV) in control theory. This comes from the process we are trying to control.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>gainDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Destination message to control the PIDController gain dynamically.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle process calls.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Reinitialize the object.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-60">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-60">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="panel">Panel</h2>
-<h4 id="value-fields-61">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nPts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of points used by panel to specify geometry</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nDims</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Dimensions used by panel to specify geometry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numNeighbors</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Neighbors of panel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>shapeId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Identifier for shape type, as used by Smoldyn</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>coords</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-61">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toNeighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Identifies neighbors of the current panel</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-61">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>neighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles incoming message from neighbor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-61">Shared message fields</h4>
-<h4 id="lookup-fields-61">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">x coordinate identified by index</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">y coordinate identified by index</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">z coordinate identified by index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="pool">Pool</h2>
-<h4 id="value-fields-62">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-62">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-62">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>increment</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Increments mol numbers by specified amount. Can be +ve or -ve</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>decrement</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Decrements mol numbers by specified amount. Can be +ve or -ve</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-62">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-62">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="poolbase">PoolBase</h2>
-<h4 id="value-fields-63">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-63">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-63">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-63">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-63">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="port">Port</h2>
-<h4 id="value-fields-64">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>scaleOutRate</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Scaling factor for outgoing rates. Applies to the RateTermscontrolled by this port. Represents a diffusion related term,or the permeability of the port</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>inStart</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Start index to S_ vector into which incoming molecules should add.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>inEnd</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">End index to S_ vector into which incoming molecules should add.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outStart</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Start index to S_ vector from where outgoing molecules come.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>outEnd</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">End index to S_ vector from where outgoing molecules come.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-64">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>availableMolsAtPort</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">Sends out the full set of molecule Ids that are available for data transfer</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>efflux</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Molecule #s going out</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>matchedMolsAtPort</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">Sends out the set of molecule Ids that match between both ports</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>efflux</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Molecule #s going out</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-64">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMatchedMolsAtPort</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Handles list of matched molecules worked out by the other port</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>influx</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Molecule #s coming back in</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleAvailableMolsAtPort</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Handles list of all species that the other port cares about</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>influx</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Molecule #s coming back in</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-64">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>port1</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for port. This one initiates the request forsetting up the communications between the portsThe shared message also handles the runtime data transfer</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>port2</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for port. This one responds to the request forsetting up the communications between the portsThe shared message also handles the runtime data transfer</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-64">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="pulsegen">PulseGen</h2>
-<h4 id="value-fields-65">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Output amplitude</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>baseLevel</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Basal level of the stimulus</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>firstLevel</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Amplitude of the first pulse in a sequence</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>firstWidth</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Width of the first pulse in a sequence</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>firstDelay</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Delay to start of the first pulse in a sequence</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>secondLevel</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Amplitude of the second pulse in a sequence</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>secondWidth</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Width of the second pulse in a sequence</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>secondDelay</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Delay to start of of the second pulse in a sequence</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>count</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of pulses in a sequence</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>trigMode</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Trigger mode for pulses in the sequence.</td>
-</tr>
-<tr class="odd">
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">0 : free-running mode where it keeps looping its output</td>
-</tr>
-<tr class="even">
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">1 : external trigger, where it is triggered by an external input (and stops after creating the first train of pulses)</td>
-</tr>
-<tr class="odd">
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">2 : external gate mode, where it keeps generating the pulses in a loop as long as the input is high.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-65">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current output level.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-65">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>input</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handle incoming input that determines gating/triggering onset.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>levelIn</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Handle level value coming from other objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>widthIn</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Handle width value coming from other objects</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>delayIn</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Handle delay value coming from other objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call, updates internal time stamp.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-65">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-65">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>level</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Level of the pulse at specified index</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>width</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Width of the pulse at specified index</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>delay</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Delay of the pulse at specified index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="rc">RC</h2>
-<h4 id="value-fields-66">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>V0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of 'state'</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>R</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Series resistance of the RC circuit.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>C</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Parallel capacitance of the RC circuit.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>state</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Output value of the RC circuit. This is the voltage across the capacitor.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>inject</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Input value to the RC circuit.This is handled as an input current to the circuit.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-66">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current output level.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-66">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>injectIn</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Receives input to the RC circuit. All incoming messages are summed up to give the total input current.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle reinitialization</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-66">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-66">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="reac">Reac</h2>
-<h4 id="value-fields-67">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kf</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant, in # units</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>kb</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse rate constant, in # units</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Kf</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant, in concentration units</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Kb</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse rate constant, in concentration units</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates of reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numProducts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of products of reaction</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-67">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-67">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the reac to recompute its numRates, as remeshing has happened</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-67">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-67">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="reacbase">ReacBase</h2>
-<h4 id="value-fields-68">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kf</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant, in # units</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>kb</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse rate constant, in # units</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Kf</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant, in concentration units</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Kb</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse rate constant, in concentration units</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates of reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numProducts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of products of reaction</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-68">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-68">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the reac to recompute its numRates, as remeshing has happened</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-68">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-68">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="rectpanel">RectPanel</h2>
-<h4 id="value-fields-69">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nPts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of points used by panel to specify geometry</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nDims</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Dimensions used by panel to specify geometry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numNeighbors</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Neighbors of panel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>shapeId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Identifier for shape type, as used by Smoldyn</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>coords</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-69">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toNeighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Identifies neighbors of the current panel</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-69">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>neighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles incoming message from neighbor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-69">Shared message fields</h4>
-<h4 id="lookup-fields-69">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">x coordinate identified by index</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">y coordinate identified by index</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">z coordinate identified by index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="reducemsg">ReduceMsg</h2>
-<h4 id="value-fields-70">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>e1</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>e2</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>i1</code></strong></td>
-<td align="left"><code>DataId</code></td>
-<td align="left">DataId of source Element.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-70">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-70">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-70">Shared message fields</h4>
-<h4 id="lookup-fields-70">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="shell">Shell</h2>
-<h4 id="value-fields-71">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-71">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reduceArraySize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Look up maximum value of an index, here ragged array size,across many nodes, and assign uniformly to all nodes. Normallyfollowed by an operation to assign the size to the object thatwas resized.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestCreate</code></strong></td>
-<td align="left"><code>string,Id,Id,string,vector<int></code></td>
-<td align="left">requestCreate( class, parent, newElm, name, dimensions ): creates a new Element on all nodes with the specified Id. Initiates a callback to indicate completion of operation. Goes to all nodes including self.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestDelete</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">requestDelete( doomedElement ):Deletes specified Element on all nodes.Initiates a callback to indicate completion of operation.Goes to all nodes including self.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestAddMsg</code></strong></td>
-<td align="left"><code>string,unsigned int,ObjId,string,ObjId,string</code></td>
-<td align="left">requestAddMsg( type, src, srcField, dest, destField );Creates specified Msg between specified Element on all nodes.Initiates a callback to indicate completion of operation.Goes to all nodes including self.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestQuit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">requestQuit():Emerges from the inner loop, and wraps up. No return value.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>move</code></strong></td>
-<td align="left"><code>Id,Id</code></td>
-<td align="left">move( origId, newParent);Moves origId to become a child of newParent</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>copy</code></strong></td>
-<td align="left"><code>vector<Id>,string,unsigned int,bool,bool</code></td>
-<td align="left">copy( origId, newParent, numRepeats, toGlobal, copyExtMsg );Copies origId to become a child of newParent</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>useClock</code></strong></td>
-<td align="left"><code>string,string,unsigned int</code></td>
-<td align="left">useClock( path, field, tick# );Specifies which clock tick to use for all elements in Path.The 'field' is typically process, but some cases need to sendupdates to the 'init' field.Tick # specifies which tick to be attached to the objects.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>sync</code></strong></td>
-<td align="left"><code>Id,unsigned int</code></td>
-<td align="left">sync( ElementId, FuncId );Synchronizes Element data indexing across all nodes.Used when distributed ops like message setup might set updifferent #s of data entries on Elements on different nodes.The ElementId is the element being synchronized.The FuncId is the 'get' function for the synchronized field.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestReMesh</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">requestReMesh( meshId );Chops up specified mesh.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSetParserIdleFlag</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">SetParserIdleFlag( bool isParserIdle );When True, the main ProcessLoop waits a little each cycleso as to avoid pounding on the CPU.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ack</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">ack( unsigned int node#, unsigned int status ):Acknowledges receipt and completion of a command on a worker node.Goes back only to master node.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestStart</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">requestStart( runtime ):Starts a simulation. Goes to all nodes including self.Initiates a callback to indicate completion of run.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestStep</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">requestStep():Advances a simulation for the specified # of steps.Goes to all nodes including self.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestStop</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">requestStop():Gently stops a simulation after completing current ops.After this op it is save to do 'start' again, and it willresume where it left offGoes to all nodes including self.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestSetupTick</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">requestSetupTick():Asks the Clock to coordinate the assignment of a specificclock tick. Args: Tick#, dt.Goes to all nodes including self.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestReinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">requestReinit():Reinits a simulation: sets to time 0.If simulation is running it stops it first.Goes to all nodes including self.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-71">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>receiveGet</code></strong></td>
-<td align="left"><code>bad</code></td>
-<td align="left">receiveGet( Uint node#, Uint status, PrepackedBuffer data )Function on master shell that handles the value relayed from worker.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>setclock</code></strong></td>
-<td align="left"><code>unsigned int,double,bool</code></td>
-<td align="left">Assigns clock ticks. Args: tick#, dt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleAck</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">Keeps track of # of acks to a blocking shell command. Arg: Source node num.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>create</code></strong></td>
-<td align="left"><code>string,Id,Id,string,vector<int></code></td>
-<td align="left">create( class, parent, newElm, name, dimensions )</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>delete</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Destroys Element, all its messages, and all its children. Args: Id</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleAddMsg</code></strong></td>
-<td align="left"><code>string,unsigned int,ObjId,string,ObjId,string</code></td>
-<td align="left">Makes a msg</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleQuit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Stops simulation running and quits the simulator</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>move</code></strong></td>
-<td align="left"><code>Id,Id</code></td>
-<td align="left">handleMove( Id orig, Id newParent ): moves an Element to a new parent</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleCopy</code></strong></td>
-<td align="left"><code>vector<Id>,string,unsigned int,bool,bool</code></td>
-<td align="left">handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): The vector< Id > has Id orig, Id newParent, Id newElm. This function copies an Element and all its children to a new parent. May also expand out the original into nCopies copies. Normally all messages within the copy tree are also copied. If the flag copyExtMsgs is true, then all msgs going out are also copied.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleUseClock</code></strong></td>
-<td align="left"><code>string,string,unsigned int</code></td>
-<td align="left">Deals with assignment of path to a given clock.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleSync</code></strong></td>
-<td align="left"><code>Id,unsigned int</code></td>
-<td align="left">handleSync( Id Element): Synchronizes DataHandler indexing across nodesThe ElementId is the element being synchronized.The FuncId is the 'get' function for the synchronized field.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleReMesh</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">handleReMesh( Id BaseMesh): Deals with outcome of resizing the meshing in a cellularcompartment (the ChemMesh class). The mesh change has topropagate down to the molecules and reactions managed by this.Mesh. The ElementId is the mesh being synchronized.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleSetParserIdleFlag</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">handleSetParserIdleFlag( bool isParserIdle ): When True, tells the ProcessLoop to wait as the Parser is idle.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleAck</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">Keeps track of # of acks to a blocking shell command. Arg: Source node num.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-71">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>master</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Issues commands from master shell to worker shells located on different nodes. Also handles acknowledgements from them.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>worker</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles commands arriving from master shell on node 0.Sends out acknowledgements from them.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>clockControl</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Controls the system Clock</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-71">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="simmanager">SimManager</h2>
-<h4 id="value-fields-72">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>syncTime</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">SyncTime is the interval between synchronizing solvers5 msec is a typical value</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>autoPlot</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">When the autoPlot flag is true, the simManager guesses whichplots are of interest, and builds them.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>plotDt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">plotDt is the timestep for plotting variables. As most will bechemical, a default of 1 sec is reasonable</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>runTime</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">runTime is the requested duration of the simulation that is stored in some kinds of model definition files.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>method</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">method is the numerical method used for the calculations.This will set up or even replace the solver with one ableto use the specified method. Currently works only with two solvers: GSL and GSSA.The GSL solver has a variety of ODE methods, by defaultRunge-Kutta-Fehlberg.The GSSA solver currently uses the Gillespie StochasticSystems Algorithm, somewhat optimized over the originalmethod.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>version</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Numerical version number. Used by kkit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>modelFamily</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Family classification of model: <em>kinetic, and </em>neuron are the options so far. In due course expect to see thingslike detailedNetwork, intFireNetwork, sigNeur and so on.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-72">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestMeshStats</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Asks for basic stats for mesh:Total # of entries, and a vector of unique volumes of voxels</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nodeInfo</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">Sends out # of nodes to use for meshing, and # of threads to use on each node, to the ChemMesh. These numbers sometimesdiffer from the total # of nodes and threads, because the SimManager may have other portions of the model to allocate.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-72">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>build</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Sets up model, with the specified method. The method may beempty if the intention is that methods be set up through hints in the ChemMesh compartments.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>makeStandardElements</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Sets up the usual infrastructure for a model, with theChemMesh, Stoich, solver and suitable messaging.The argument is the MeshClass to use.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>meshSplit</code></strong></td>
-<td align="left"><code>double,vector<unsigned int>,vector<unsigned int>,vector<unsigned int>,vector<unsigned int></code></td>
-<td align="left">Handles message from ChemMesh that defines howmeshEntries communicate between nodes.First arg is oldvol, next is list of other nodes, third arg is list number ofmeshEntries to be transferred for each of these nodes, fourth arg is catenated list of meshEntries indices onmy node going to each of the other connected nodes, andlast arg is matching list of meshEntries on other nodes</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>meshStats</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">Basic statistics for mesh: Total # of entries, and a vectorof unique volumes of voxels</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-72">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>nodeMeshing</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to ChemMesh to coordinate meshing with paralleldecomposition and with the Stoich</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-72">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="singlemsg">SingleMsg</h2>
-<h4 id="value-fields-73">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>e1</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>e2</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>i1</code></strong></td>
-<td align="left"><code>DataId</code></td>
-<td align="left">Index of source object.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>i2</code></strong></td>
-<td align="left"><code>DataId</code></td>
-<td align="left">Index of dest object.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-73">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-73">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-73">Shared message fields</h4>
-<h4 id="lookup-fields-73">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="solverjunction">SolverJunction</h2>
-<h4 id="value-fields-74">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numReacs</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of cross-compartment reactions on this Junction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numDiffMols</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of molecule species diffusing across this Junction</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numMeshEntries</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of voxels (mesh entries) handled by Junction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>otherCompartment</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of compartment on other side of this Junction. Readily obtained by message traversal, just a utility field.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-74">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>junctionPoolNum</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Sends out vector of all mol #s needed to compute junction rates.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>junctionPoolDelta</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Sends out vector of all mol # changes going across junction.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>junctionPoolNum</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Sends out vector of all mol #s needed to compute junction rates.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-74">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleJunctionPoolNum</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Handles vector of doubles specifying pool num, that arrive at the Junction, by redirecting up to parent StoichPools object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleJunctionPoolNum</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Handles vector of doubles specifying pool num, that arrive at the Junction, by redirecting up to parent StoichPools object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleJunctionPoolDelta</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">Handles vector of doubles with pool num changes that arrive at the Junction, by redirecting up to parent StoichPools object</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-74">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>symJunction</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Symmetric shared message between SolverJunctions to handle cross-solver reactions and diffusion. This variant sends only pool mol#s, and is symmetric.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>masterJunction</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message between SolverJunctions to handle cross-solver reactions and diffusion. This sends the change in pool #, of abutting voxels, and receives the pool# of the same abutting voxels. Thus it operates on the solver that is doing the diffusion calculations. This will typically be the solver that operates at a finer level of detail. The order of detail is Smoldyn > Gillespie > deterministic. For two identical solvers we would typically have one with the finer grid size become the master Junction.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>followerJunction</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message between SolverJunctions to handle cross-solver reactions and diffusion. This sends the pool #, of its boundary voxels, and receives back changes in the pool# of the same boundary voxels voxels. Thus it operates on the solver that is just tracking the diffusion calculations that the other (master) solver is doing</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-74">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="sparsemsg">SparseMsg</h2>
-<h4 id="value-fields-75">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>e1</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>e2</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Id of source Element.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>srcFieldsOnE2</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>destFieldsOnE1</code></strong></td>
-<td align="left"><code>vector<string></code></td>
-<td align="left">Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numRows</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of rows in matrix.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numColumns</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of columns in matrix.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numEntries</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Entries in matrix.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>probability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">connection probability for random connectivity.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>seed</code></strong></td>
-<td align="left"><code>long</code></td>
-<td align="left">Random number seed for generating probabilistic connectivity.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-75">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-75">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>setRandomConnectivity</code></strong></td>
-<td align="left"><code>double,long</code></td>
-<td align="left">Assigns connectivity with specified probability and seed</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>setEntry</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int,unsigned int</code></td>
-<td align="left">Assigns single row,column value</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>unsetEntry</code></strong></td>
-<td align="left"><code>unsigned int,unsigned int</code></td>
-<td align="left">Clears single row,column entry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>clear</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Clears out the entire matrix</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>transpose</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Transposes the sparse matrix</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-75">Shared message fields</h4>
-<h4 id="lookup-fields-75">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="species">Species</h2>
-<h4 id="value-fields-76">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>molWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Molecular weight of species</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-76">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>sendMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">returns molWt.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-76">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWtRequest</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle requests for molWt.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-76">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>pool</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to pools of this Species type</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-76">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="spherepanel">SpherePanel</h2>
-<h4 id="value-fields-77">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nPts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of points used by panel to specify geometry</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nDims</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Dimensions used by panel to specify geometry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numNeighbors</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Neighbors of panel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>shapeId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Identifier for shape type, as used by Smoldyn</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>coords</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-77">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toNeighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Identifies neighbors of the current panel</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-77">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>neighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles incoming message from neighbor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-77">Shared message fields</h4>
-<h4 id="lookup-fields-77">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">x coordinate identified by index</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">y coordinate identified by index</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">z coordinate identified by index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="spikegen">SpikeGen</h2>
-<h4 id="value-fields-78">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>threshold</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Spiking threshold, must cross it going up</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>refractT</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Refractory Time.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>abs_refract</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Absolute refractory time. Synonym for refractT.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>hasFired</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">True if SpikeGen has just fired</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>edgeTriggered</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">When edgeTriggered = 0, the SpikeGen will fire an event in each timestep while incoming Vm is > threshold and at least abs_refracttime has passed since last event. This may be problematic if the incoming Vm remains above threshold for longer than abs_refract. Setting edgeTriggered to 1 resolves this as the SpikeGen generatesan event only on the rising edge of the incoming Vm and will remain idle unless the incoming Vm goes below threshold.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-78">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>event</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out a trigger for an event.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-78">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-78">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message to receive Process message from scheduler</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-78">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="stats">Stats</h2>
-<h4 id="value-fields-79">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>mean</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Mean of all sampled values.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>sdev</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Standard Deviation of all sampled values.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>sum</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sum of all sampled values.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>num</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of all sampled values.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-79">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reduce</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Execute statistics reduction operation on all targets andplace results in this object</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-79">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>trig</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Triggers Reduction operation.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-79">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-79">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="stimulustable">StimulusTable</h2>
-<h4 id="value-fields-80">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>vec</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">vector with all table entries</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputValue</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Output value holding current table entry or output of a calculation</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>startTime</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Start time used when table is emitting values. For lookupvalues below this, the table just sends out its zero entry.Corresponds to zeroth entry of table.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>stopTime</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Time to stop emitting values.If time exceeds this, then the table sends out its last entry.The stopTime corresponds to the last entry of table.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>loopTime</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">If looping, this is the time between successive cycle starts.Defaults to the difference between stopTime and startTime, so that the output waveform cycles with precisely the same duration as the table contents.If larger than stopTime - startTime, then it pauses at the last table value till it is time to go around again.If smaller than stopTime - startTime, then it begins the next cycle even before the first one has reached the end of the table.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>stepSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Increment in lookup (x) value on every timestep. If it isless than or equal to zero, the StimulusTable uses the current timeas the lookup value.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>stepPosition</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current value of lookup (x) value.If stepSize is less than or equal to zero, this is set tothe current time to use as the lookup value.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>doLoop</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag: Should it loop around to startTime once it has reachedstopTime. Default (zero) is to do a single pass.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-80">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out tabulated data according to lookup parameters.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-80">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>linearTransform</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Linearly scales and offsets data. Scale first, then offset.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>xplot</code></strong></td>
-<td align="left"><code>string,string</code></td>
-<td align="left">Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>plainPlot</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>loadCSV</code></strong></td>
-<td align="left"><code>string,int,int,char</code></td>
-<td align="left">Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>loadXplot</code></strong></td>
-<td align="left"><code>string,string</code></td>
-<td align="left">Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>loadXplotRange</code></strong></td>
-<td align="left"><code>string,string,unsigned int,unsigned int</code></td>
-<td align="left">Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>compareXplot</code></strong></td>
-<td align="left"><code>string,string,string</code></td>
-<td align="left">Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>compareVec</code></strong></td>
-<td align="left"><code>vector<double>,string</code></td>
-<td align="left">Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>clearVec</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles request to clear the data vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call, updates internal time stamp.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-80">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-80">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Value of table at specified index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="stoich">Stoich</h2>
-<h4 id="value-fields-81">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>useOneWayReacs</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nVarPools</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of variable molecule pools in the reac system</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numMeshEntries</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of meshEntries in reac-diff system</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>estimatedDt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Path of reaction system to take over</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-81">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>plugin</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Sends out Stoich Id so that plugins can directly access fields and functions</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nodeDiffBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Sends mol #s across boundary between nodes, to calculate diffusionterms. arg1 is originating node, arg2 is list of meshIndices forwhich data is being transferred, and arg3 are the 'n' values forall the pools on the specified meshIndices, to be plugged intothe appropriate place on the recipient node's S_ matrix</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>poolsReactingAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">A vector of mol counts (n) of those pools that react across a boundary. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacRollbacksAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">Occasionally, a Gillespie advance will cause the mol conc on the target stoich side to become negative. If so, this message does a patch up job by telling the originating Stoich to roll back to the specified number of reac firings, which is the max that the target was able to handle. This is probably numerically naughty, but it is better than negative concentrations</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reacRatesAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">A vector of reac rates (V) of each reaction crossing the boundary between compartments. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. In the case of Gillespie calculations <em>V</em> is the integer # of transitions (firings) of each reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-81">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>meshSplit</code></strong></td>
-<td align="left"><code>double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> ></code></td>
-<td align="left">Handles message from ChemMesh that defines how meshEntries are decomposed on this node, and how they communicate between nodes.Args: (oldVol, volumeVectorForAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#])</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleReacRatesAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handlePoolsReactingAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of pool #s for every pool that reacts across the boundary, in every mesh entry. that reacts across a boundary, in every mesh entry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleReacRollbacksAcrossBoundary</code></strong></td>
-<td align="left"><code>unsigned int,vector<double></code></td>
-<td align="left">When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. Only one side does the calculations to assure mass conservation. There are rare cases when the calculations of one solver, typically a Gillespie one, gives such a large change that the concentrations on the other side would become negative in one or more molecules This message handles such cases on the Gillespie side, by telling the solver to roll back its recent calculation and instead use the specified vector for the rates, that is the # of mols changed in the latest timestep. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-81">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>boundaryReacOut</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>boundaryReacIn</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-81">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="stoichcore">StoichCore</h2>
-<h4 id="value-fields-82">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>useOneWayReacs</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nVarPools</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of variable molecule pools in the reac system</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>estimatedDt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Path of reaction system to take over</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-82">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-82">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-82">Shared message fields</h4>
-<h4 id="lookup-fields-82">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="stoichpools">StoichPools</h2>
-<p><strong>Author</strong>: Upinder S. Bhalla, 2012, NCBS</p>
-<p><strong>Description</strong>: Pure virtual base class for handling reaction pools. GslStoich is derived from this.</p>
-<h4 id="value-fields-83">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-83">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-83">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>addJunction</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Add a junction between the current solver and the one whose Id is passed in.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>dropJunction</code></strong></td>
-<td align="left"><code>Id</code></td>
-<td align="left">Drops a junction between the current solver and the one whose Id is passed in. Ignores if no junction.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-83">Shared message fields</h4>
-<h4 id="lookup-fields-83">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="sumfunc">SumFunc</h2>
-<p><strong>Author</strong>: Upi Bhalla</p>
-<p><strong>Description</strong>: SumFunc object. Adds up all inputs</p>
-<h4 id="value-fields-84">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>result</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Outcome of function computation</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-84">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out sum on each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-84">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>input</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-84">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-84">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="surface">Surface</h2>
-<h4 id="value-fields-85">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>volume</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">This is something I'll need to write a function to compute.Perhaps have an update routine as it may be hard to compute but is needed often by the molecules.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-85">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>absorb</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">these help the system define non-standard operations for what a molecule does when it hits a surface.The default is reflect.As a molecule may interact with multiple surfaces, it isn't enough to confer a property on the molecule itself. We have to use messages. Perhaps we don't need these, but instead put entities on the surface which the molecule interacts with if it doesn't do the basic reflect operation.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>transmit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Surface lets molecules through</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>jump</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">dunno</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>mixture</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">dunno</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>surface</code></strong></td>
-<td align="left"><code>double,double,double</code></td>
-<td align="left">Connects up to a compartment, either as interior or exterior Args are volume, area, perimeter</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-85">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-85">Shared message fields</h4>
-<h4 id="lookup-fields-85">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="symcompartment">SymCompartment</h2>
-<h4 id="value-fields-86">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">membrane potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Cm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane capacitance</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Em</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Resting membrane potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Im</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current going through membrane</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>inject</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current injection to deliver into compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>initVm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value for membrane potential</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Rm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane resistance</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ra</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Axial resistance of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diameter</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diameter of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>length</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Length of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>x0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">X coordinate of start of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Y coordinate of start of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>z0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Z coordinate of start of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">x coordinate of end of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">y coordinate of end of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">z coordinate of end of compartment</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-86">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>VmOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Vm value of compartment on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>axialOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Vm value of compartment to adjacent compartments,on each timestep</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>raxialOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out Raxial information on each timestep, fields are Ra and Vm</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>raxialOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out Ra and Vm on each timestep</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>sumRaxialOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Ra</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestSumAxial</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Sends out request for Ra.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>raxialOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out Ra and Vm on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>sumRaxialOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Ra</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSumAxial</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Sends out request for Ra.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Raxial2Out</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out Ra and Vm</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>sumRaxial2Out</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Ra</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestSumAxial2</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Sends out request for Ra.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Raxial2Out</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out Ra and Vm</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>sumRaxial2Out</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Ra</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSumAxial2</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Sends out request for Ra.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Raxial2Out</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out Ra and Vm</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>sumRaxial2Out</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Ra</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestSumAxial2</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Sends out request for Ra.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-86">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>injectMsg</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>randInject</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>injectMsg</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cable</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message for organizing compartments into groups, calledcables. Doesn't do anything.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'process' call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'reinit' call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>initProc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>initReinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles Reinit call for the 'init' phase of the Compartment calculations.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleChannel</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles conductance and Reversal potential arguments from Channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleRaxial</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles Raxial info: arguments are Ra and Vm.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleAxial</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Axial information. Argument is just Vm.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>raxialSym</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Expects Ra and Vm from other compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>sumRaxial</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Expects Ra from other compartment.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleSumRaxialRequest</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle request to send back Ra to originating compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-86">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process messages from the scheduler objects. The Process should be called <em>second</em> in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>init</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>axial</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>raxial</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>raxial1</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a raxial shared message between symmetric compartments.It goes from the tail of the current compartment to one closer to the soma.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>CONNECTTAIL</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a raxial shared message between symmetric compartments.It is an alias for raxial1.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>raxial2</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a raxial2 shared message between symmetric compartments.It goes from the head of the current compartment to a compartment further away from the soma</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>CONNECTHEAD</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a raxial2 shared message between symmetric compartments.It is an alias for raxial2.It goes from the current compartment to one further from the soma</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>CONNECTCROSS</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a raxial2 shared message between symmetric compartments.It is an alias for raxial2.Conceptually, this goes from the tail of the current compartment to the tail of a sibling compartment. However,this works out to the same as CONNECTHEAD in terms of equivalentcircuit.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-86">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="synbase">SynBase</h2>
-<h4 id="value-fields-87">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numSynapses</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of synapses on SynBase</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-87">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-87">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-87">Shared message fields</h4>
-<h4 id="lookup-fields-87">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="synchan">SynChan</h2>
-<h4 id="value-fields-88">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numSynapses</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of synapses on SynBase</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Gbar</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximal channel conductance</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal potential of channel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel conductance variable</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current variable</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>tau1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Decay time constant for the synaptic conductance, tau1 >= tau2.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>tau2</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Rise time constant for the synaptic conductance, tau1 >= tau2.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>normalizeWeights</code></strong></td>
-<td align="left"><code>bool</code></td>
-<td align="left">Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-88">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>permeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance term going out to GHK object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-88">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>activation</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sometimes we want to continuously activate the channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>modulator</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Modulate channel response</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-88">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message to Goldman-Hodgkin-Katz object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message to receive Process message from scheduler</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-88">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="synchanbase">SynChanBase</h2>
-<h4 id="value-fields-89">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numSynapses</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of synapses on SynBase</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Gbar</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximal channel conductance</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal potential of channel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel conductance variable</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current variable</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-89">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>permeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance term going out to GHK object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-89">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-89">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message to Goldman-Hodgkin-Katz object</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-89">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="synapse">Synapse</h2>
-<h4 id="value-fields-90">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>weight</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Synaptic weight</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>delay</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Axonal propagation delay to this synapse</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-90">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-90">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>addSpike</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles arriving spike messages, by redirecting up to parent SynBase object</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-90">Shared message fields</h4>
-<h4 id="lookup-fields-90">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="table">Table</h2>
-<h4 id="value-fields-91">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>vec</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">vector with all table entries</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputValue</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Output value holding current table entry or output of a calculation</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>threshold</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">threshold used when Table acts as a buffer for spikes</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-91">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestData</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Sends request for a field to target object</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-91">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>linearTransform</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Linearly scales and offsets data. Scale first, then offset.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>xplot</code></strong></td>
-<td align="left"><code>string,string</code></td>
-<td align="left">Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>plainPlot</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>loadCSV</code></strong></td>
-<td align="left"><code>string,int,int,char</code></td>
-<td align="left">Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>loadXplot</code></strong></td>
-<td align="left"><code>string,string</code></td>
-<td align="left">Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>loadXplotRange</code></strong></td>
-<td align="left"><code>string,string,unsigned int,unsigned int</code></td>
-<td align="left">Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>compareXplot</code></strong></td>
-<td align="left"><code>string,string,string</code></td>
-<td align="left">Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>compareVec</code></strong></td>
-<td align="left"><code>vector<double>,string</code></td>
-<td align="left">Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>clearVec</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles request to clear the data vector</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>input</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Fills data into the Table.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>spike</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Fills spike timings into the Table. Signal has to exceed thresh</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>recvData</code></strong></td>
-<td align="left"><code>bad</code></td>
-<td align="left">Handles data sent back following request</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call, updates internal time stamp.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-91">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-91">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Value of table at specified index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="tablebase">TableBase</h2>
-<h4 id="value-fields-92">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>vec</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">vector with all table entries</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>outputValue</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Output value holding current table entry or output of a calculation</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-92">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-92">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>linearTransform</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Linearly scales and offsets data. Scale first, then offset.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>xplot</code></strong></td>
-<td align="left"><code>string,string</code></td>
-<td align="left">Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>plainPlot</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>loadCSV</code></strong></td>
-<td align="left"><code>string,int,int,char</code></td>
-<td align="left">Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>loadXplot</code></strong></td>
-<td align="left"><code>string,string</code></td>
-<td align="left">Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>loadXplotRange</code></strong></td>
-<td align="left"><code>string,string,unsigned int,unsigned int</code></td>
-<td align="left">Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>compareXplot</code></strong></td>
-<td align="left"><code>string,string,string</code></td>
-<td align="left">Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>compareVec</code></strong></td>
-<td align="left"><code>vector<double>,string</code></td>
-<td align="left">Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>clearVec</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles request to clear the data vector</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-92">Shared message fields</h4>
-<h4 id="lookup-fields-92">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Value of table at specified index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="tableentry">TableEntry</h2>
-<h4 id="value-fields-93">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>value</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Data value in this entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-93">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-93">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-93">Shared message fields</h4>
-<h4 id="lookup-fields-93">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="tick">Tick</h2>
-<h4 id="value-fields-94">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>dt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Timestep for this tick</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>localdt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Timestep for this tick</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-94">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process0</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 0</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit0</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 0</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process1</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit1</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 1</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process2</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 2</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit2</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 2</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process3</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 3</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit3</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 3</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process4</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 4</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit4</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 4</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process5</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 5</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit5</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 5</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process6</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 6</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit6</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 6</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process7</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 7</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit7</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 7</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process8</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 8</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit8</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 8</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process9</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Process for Tick 9</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit9</code></strong></td>
-<td align="left"><code>PK8ProcInfo</code></td>
-<td align="left">Reinit for Tick 9</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-94">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-94">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc0</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc1</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc2</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc3</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc4</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc5</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc6</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc7</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc8</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc9</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared proc/reinit message</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-94">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="tripanel">TriPanel</h2>
-<h4 id="value-fields-95">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>nPts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of points used by panel to specify geometry</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nDims</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Dimensions used by panel to specify geometry</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numNeighbors</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of Neighbors of panel</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>shapeId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Identifier for shape type, as used by Smoldyn</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>coords</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-95">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toNeighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Identifies neighbors of the current panel</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-95">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>neighbor</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles incoming message from neighbor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-95">Shared message fields</h4>
-<h4 id="lookup-fields-95">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">x coordinate identified by index</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">y coordinate identified by index</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">z coordinate identified by index</td>
-</tr>
-</tbody>
-</table>
-<h2 id="vectortable">VectorTable</h2>
-<h4 id="value-fields-96">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>xdivs</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of divisions.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>xmin</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Minimum value in table.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>xmax</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximum value in table.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>invdx</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximum value in table.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>table</code></strong></td>
-<td align="left"><code>vector<double></code></td>
-<td align="left">The lookup table.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-96">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-96">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-96">Shared message fields</h4>
-<h4 id="lookup-fields-96">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lookupvalue</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Lookup function that performs interpolation to return a value.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>lookupindex</code></strong></td>
-<td align="left"><code>unsigned int,double</code></td>
-<td align="left">Lookup function that returns value by index.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zbufpool">ZBufPool</h2>
-<h4 id="value-fields-97">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-97">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-97">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-97">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-97">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zenz">ZEnz</h2>
-<h4 id="value-fields-98">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Km</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numKm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in number units, volume dependent</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kcat</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant for enzyme, units 1/sec</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>k1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward reaction from enz + sub to complex</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>k2</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse reaction from complex to enz + sub</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>k3</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant from complex to product + enz</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ratio</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Ratio of k2/k3</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concK1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">K1 expressed in concentration (1/millimolar.sec) units</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-98">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toEnz</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toCplx</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-98">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product. Dummy.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cplxDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of enz-sub complex</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-98">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to product molecule</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enz</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to enzyme pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cplx</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to enz-sub complex pool</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-98">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zfuncpool">ZFuncPool</h2>
-<h4 id="value-fields-99">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-99">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-99">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>input</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles input to control value of n_</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-99">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-99">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zmmenz">ZMMenz</h2>
-<h4 id="value-fields-100">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Km</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numKm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in number units, volume dependent</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kcat</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant for enzyme, units 1/sec</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-100">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-100">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product. Dummy.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-100">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to product molecule</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-100">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zpool">ZPool</h2>
-<h4 id="value-fields-101">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-101">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-101">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-101">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-101">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zreac">ZReac</h2>
-<h4 id="value-fields-102">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kf</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant, in # units</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>kb</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse rate constant, in # units</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Kf</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant, in concentration units</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Kb</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse rate constant, in concentration units</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates of reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numProducts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of products of reaction</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-102">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-102">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the reac to recompute its numRates, as remeshing has happened</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-102">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-102">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombiebufpool">ZombieBufPool</h2>
-<h4 id="value-fields-103">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-103">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-103">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-103">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-103">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombiecaconc">ZombieCaConc</h2>
-<h4 id="value-fields-104">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ca</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Calcium concentration.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>CaBasal</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Basal Calcium concentration.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Ca_base</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Basal Calcium concentration, synonym for CaBasal</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>tau</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Settling time for Ca concentration</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>B</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Volume scaling factor</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>thick</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Thickness of Ca shell.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>ceiling</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>floor</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Floor value for Ca concentration. If Ca < floor, Ca = floor</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-104">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>concOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of Ca in pool</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-104">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>current</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Calcium Ion current, due to be converted to conc.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>currentFraction</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Fraction of total Ion current, that is carried by Ca2+.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>increase</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Any input current that increases the concentration.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>decrease</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Any input current that decreases the concentration.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>basal</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Synonym for assignment of basal conc.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-104">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message to receive Process message from scheduler</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-104">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombiecompartment">ZombieCompartment</h2>
-<h4 id="value-fields-105">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">membrane potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Cm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane capacitance</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Em</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Resting membrane potential</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Im</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current going through membrane</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>inject</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Current injection to deliver into compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>initVm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value for membrane potential</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Rm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Membrane resistance</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ra</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Axial resistance of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diameter</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diameter of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>length</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Length of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>x0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">X coordinate of start of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>y0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Y coordinate of start of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>z0</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Z coordinate of start of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>x</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">x coordinate of end of compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>y</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">y coordinate of end of compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>z</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">z coordinate of end of compartment</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-105">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>VmOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Vm value of compartment on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>axialOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out Vm value of compartment to adjacent compartments,on each timestep</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>raxialOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out Raxial information on each timestep, fields are Ra and Vm</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-105">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>injectMsg</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>randInject</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>injectMsg</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cable</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message for organizing compartments into groups, calledcables. Doesn't do anything.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'process' call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles 'reinit' call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>initProc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>initReinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles Reinit call for the 'init' phase of the Compartment calculations.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleChannel</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles conductance and Reversal potential arguments from Channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>handleRaxial</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles Raxial info: arguments are Ra and Vm.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleAxial</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Axial information. Argument is just Vm.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-105">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process messages from the scheduler objects. The Process should be called <em>second</em> in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>init</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>axial</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>raxial</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-105">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombieenz">ZombieEnz</h2>
-<h4 id="value-fields-106">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Km</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numKm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in number units, volume dependent</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kcat</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant for enzyme, units 1/sec</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>k1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward reaction from enz + sub to complex</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>k2</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse reaction from complex to enz + sub</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>k3</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant from complex to product + enz</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ratio</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Ratio of k2/k3</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concK1</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">K1 expressed in concentration (1/millimolar.sec) units</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-106">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toEnz</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toCplx</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-106">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product. Dummy.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cplxDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of enz-sub complex</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-106">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to product molecule</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enz</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to enzyme pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>cplx</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to enz-sub complex pool</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-106">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombiefuncpool">ZombieFuncPool</h2>
-<h4 id="value-fields-107">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-107">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-107">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>input</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles input to control value of n_</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-107">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-107">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombiehhchannel">ZombieHHChannel</h2>
-<h4 id="value-fields-108">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gbar</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Maximal channel conductance</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ek</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reversal potential of channel</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Gk</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel conductance variable</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ik</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current variable</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Xpower</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Power for X gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Ypower</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Power for Y gate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Zpower</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Power for Z gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>instant</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>X</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">State variable for X gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Y</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">State variable for Y gate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Z</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">State variable for Y gate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>useConcentration</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Flag: when true, use concentration message rather than Vm tocontrol Z gate</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-108">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>channelOut</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends channel variables Gk and Ek to compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>permeability</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Conductance term going out to GHK object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>IkOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Channel current. This message typically goes to concenobjects that keep track of ion concentration.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-108">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Vm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles Vm message coming in from compartment</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>concen</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Incoming message from Concen object to specific conc to usein the Z gate calculations</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>createGate</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Function to create specified gate.Argument: Gate type [X Y Z]</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-108">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>channel</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>ghk</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Message to Goldman-Hodgkin-Katz object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</td>
-</tr>
-<tr class="even">
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-108">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombiemmenz">ZombieMMenz</h2>
-<h4 id="value-fields-109">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Km</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in SI conc units (milliMolar)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numKm</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Michaelis-Menten constant in number units, volume dependent</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kcat</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant for enzyme, units 1/sec</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-109">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-109">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>enzDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of Enzyme</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product. Dummy.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the MMEnz to recompute its numKm after remeshing</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-109">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to product molecule</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-109">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombiepool">ZombiePool</h2>
-<h4 id="value-fields-110">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>n</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Number of molecules in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of number of molecules in pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>diffConst</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Diffusion constant of molecule</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>conc</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Concentration of molecules in this pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>concInit</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Initial value of molecular concentration in pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>size</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>speciesId</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Species identifier for this mol pool. Eventually link to ontology.</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-110">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>nOut</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out # of molecules in pool on each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>requestMolWt</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Requests Species object for mol wt</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>requestSize</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Requests Size of pool from matching mesh entry</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-110">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>group</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handle for grouping. Doesn't do anything.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reacDest</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Handles reaction input</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>handleMolWt</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>double,unsigned int,unsigned int,vector<unsigned int>,vector<double></code></td>
-<td align="left">Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-110">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>reac</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>species</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for connecting to species objects</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>mesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for dealing with mesh operations</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-110">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombiereac">ZombieReac</h2>
-<h4 id="value-fields-111">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>kf</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant, in # units</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>kb</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse rate constant, in # units</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>Kf</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Forward rate constant, in concentration units</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>Kb</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Reverse rate constant, in concentration units</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>numSubstrates</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of substrates of reaction</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>numProducts</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Number of products of reaction</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-111">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>toSub</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>toPrd</code></strong></td>
-<td align="left"><code>double,double</code></td>
-<td align="left">Sends out increment of molecules on product each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-111">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>subDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of substrate</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>prdDest</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles # of molecules of product</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>remesh</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Tells the reac to recompute its numRates, as remeshing has happened</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-111">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>sub</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate pool</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>prd</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Connects to substrate pool</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-111">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="zombiesumfunc">ZombieSumFunc</h2>
-<h4 id="value-fields-112">Value fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>this</code></strong></td>
-<td align="left"><code>Neutral</code></td>
-<td align="left">Access function for entire object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>name</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Name of object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>me</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">ObjId for current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>parent</code></strong></td>
-<td align="left"><code>ObjId</code></td>
-<td align="left">Parent ObjId for current object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>children</code></strong></td>
-<td align="left"><code>vector<Id></code></td>
-<td align="left">vector of ObjIds listing all children of current object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>path</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">text path for object</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>class</code></strong></td>
-<td align="left"><code>string</code></td>
-<td align="left">Class Name of object</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>linearSize</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left"># of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>objectDimensions</code></strong></td>
-<td align="left"><code>vector<unsigned int></code></td>
-<td align="left">Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>lastDimension</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>localNumField</code></strong></td>
-<td align="left"><code>unsigned int</code></td>
-<td align="left">For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>pathIndices</code></strong></td>
-<td align="left"><code>vector< vector<unsigned int> ></code></td>
-<td align="left">Indices of the entire path hierarchy leading up to this Object.</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>msgOut</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages going out from this Element</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>msgIn</code></strong></td>
-<td align="left"><code>vector<ObjId></code></td>
-<td align="left">Messages coming in to this Element</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>result</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">outcome of summation</td>
-</tr>
-</tbody>
-</table>
-<h4 id="source-message-fields-112">Source message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>childMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message to child Elements</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>output</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Sends out sum on each timestep</td>
-</tr>
-</tbody>
-</table>
-<h4 id="destination-message-fields-112">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>parentMsg</code></strong></td>
-<td align="left"><code>int</code></td>
-<td align="left">Message from Parent Element(s)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>input</code></strong></td>
-<td align="left"><code>double</code></td>
-<td align="left">Handles input values</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles process call</td>
-</tr>
-<tr class="even">
-<td align="left"><strong><code>reinit</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Handles reinit call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-112">Shared message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>proc</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">Shared message for process and reinit</td>
-</tr>
-</tbody>
-</table>
-<h4 id="lookup-fields-112">Lookup fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>neighbours</code></strong></td>
-<td align="left"><code>string,vector<Id></code></td>
-<td align="left">Ids of Elements connected this Element on specified field.</td>
-</tr>
-</tbody>
-</table>
-<h2 id="testsched">testSched</h2>
-<h4 id="value-fields-113">Value fields</h4>
-<h4 id="source-message-fields-113">Source message fields</h4>
-<h4 id="destination-message-fields-113">Destination message fields</h4>
-<table>
-<thead>
-<tr class="header">
-<th align="left">Field</th>
-<th align="left">Type</th>
-<th align="left">Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong><code>process</code></strong></td>
-<td align="left"><code>void</code></td>
-<td align="left">handles process call</td>
-</tr>
-</tbody>
-</table>
-<h4 id="shared-message-fields-113">Shared message fields</h4>
-<h4 id="lookup-fields-113">Lookup fields</h4>
-<h1 id="moose-functions">MOOSE Functions</h1>
-<h2 id="ce">ce</h2>
-<p>Set the current working element. 'ce' is an alias of this function</p>
-<h2 id="connect">connect</h2>
-<p>connect(src, src_field, dest, dest_field, message_type) -> bool</p>
-<p>Create a message between <code>src_field</code> on <code>src</code> object to <code>dest_field</code></p>
-<p>on <code>dest</code> object.</p>
-<h4 id="parameters">Parameters</h4>
-<p>src : element</p>
-<p>the source object</p>
-<p>src_field : str</p>
-<p>the source field name. Fields listed under <code>srcFinfo</code> and</p>
-<p><code>sharedFinfo</code> qualify for this.</p>
-<p>dest : element</p>
-<p>the destination object.</p>
-<p>dest_field : str</p>
-<p>the destination field name. Fields listed under <code>destFinfo</code></p>
-<p>and <code>sharedFinfo</code> qualify for this.</p>
-<p>message_type : str (optional)</p>
-<p>Type of the message. Can be <code>Single</code>, <code>OneToOne</code>, <code>OneToAll</code>.</p>
-<p>If not specified, it defaults to <code>Single</code>.</p>
-<h4 id="returns">Returns</h4>
-<p>element of the message-manager for the newly created message.</p>
-<h4 id="example">Example</h4>
-<p>Connect the output of a pulse generator to the input of a spike</p>
-<p>generator:</p>
-<pre><code>
->>> pulsegen = moose.PulseGen('pulsegen')
-
->>> spikegen = moose.SpikeGen('spikegen')
-
->>> moose.connect(pulsegen, 'outputOut', spikegen, 'Vm')
-
-1
-</code></pre>
-<h2 id="copy">copy</h2>
-<p>copy(src, dest, name, n, toGlobal, copyExtMsg) -> bool</p>
-<p>Make copies of a moose object.</p>
-<h4 id="parameters-1">Parameters</h4>
-<p>src : ematrix, element or str</p>
-<p>source object.</p>
-<p>dest : ematrix, element or str</p>
-<p>Destination object to copy into.</p>
-<p>name : str</p>
-<p>Name of the new object. If omitted, name of the original will be used.</p>
-<p>n : int</p>
-<p>Number of copies to make.</p>
-<p>toGlobal: int</p>
-<p>Relevant for parallel environments only. If false, the copies will</p>
-<p>reside on local node, otherwise all nodes get the copies.</p>
-<p>copyExtMsg: int</p>
-<p>If true, messages to/from external objects are also copied.</p>
-<h4 id="returns-1">Returns</h4>
-<p>ematrix of the copied object</p>
-<h2 id="delete">delete</h2>
-<p>moose.delete(id)</p>
-<p>Delete the underlying moose object. This does not delete any of the</p>
-<p>Python objects referring to this ematrix but does invalidate them. Any</p>
-<p>attempt to access them will raise a ValueError.</p>
-<p>Parameters</p>
-<h4 id="section"></h4>
-<p>id : ematrix</p>
-<p>ematrix of the object to be deleted.</p>
-<h2 id="element">element</h2>
-<p>moose.element(arg) -> moose object</p>
-<p>Convert a path or an object to the appropriate builtin moose class</p>
-<p>instance</p>
-<h4 id="parameters-2">Parameters</h4>
-<p>arg: str or ematrix or moose object</p>
-<p>path of the moose element to be converted or another element (possibly</p>
-<p>available as a superclass instance).</p>
-<h4 id="returns-2">Returns</h4>
-<p>An element of the moose builtin class the specified object belongs</p>
-<p>to.</p>
-<h2 id="exists">exists</h2>
-<p>True if there is an object with specified path.</p>
-<h2 id="getcwe">getCwe</h2>
-<p>Get the current working element. 'pwe' is an alias of this function.</p>
-<h2 id="getfield">getField</h2>
-<p>getField(element, field, fieldtype) -- Get specified field of specified type from object ematrix.</p>
-<h2 id="getfielddict">getFieldDict</h2>
-<p>getFieldDict(className, finfoType) -> dict</p>
-<p>Get dictionary of field names and types for specified class.</p>
-<h4 id="parameters-3">Parameters</h4>
-<p>className : str</p>
-<p>MOOSE class to find the fields of.</p>
-<p>finfoType : str (optional)</p>
-<p>Finfo type of the fields to find. If empty or not specified, all</p>
-<p>fields will be retrieved.</p>
-<p>note: This behaviour is different from <code>getFieldNames</code> where only</p>
-<p><code>valueFinfo</code>s are returned when <code>finfoType</code> remains unspecified.</p>
-<h4 id="example-1">Example</h4>
-<p>List all the source fields on class Neutral:</p>
-<pre><code>
->>> moose.getFieldDict('Neutral', 'srcFinfo')
-
-{'childMsg': 'int'}
-</code></pre>
-<h2 id="getfieldnames">getFieldNames</h2>
-<p>getFieldNames(className, finfoType='valueFinfo') -> tuple</p>
-<p>Get a tuple containing the name of all the fields of <code>finfoType</code></p>
-<p>kind.</p>
-<h4 id="parameters-4">Parameters</h4>
-<p>className : string</p>
-<p>Name of the class to look up.</p>
-<p>finfoType : string</p>
-<p>The kind of field (<code>valueFinfo</code>, <code>srcFinfo</code>, <code>destFinfo</code>,</p>
-<p><code>lookupFinfo</code>, <code>fieldElementFinfo</code>.).</p>
-<h2 id="isrunning">isRunning</h2>
-<p>True if the simulation is currently running.</p>
-<h2 id="loadmodel">loadModel</h2>
-<p>loadModel(filename, modelpath, solverclass) -> moose.ematrix</p>
-<p>Load model from a file to a specified path.</p>
-<h4 id="parameters-5">Parameters</h4>
-<p>filename : str</p>
-<p>model description file.</p>
-<p>modelpath : str</p>
-<p>moose path for the top level element of the model to be created.</p>
-<p>solverclass : str</p>
-<p>(optional) solver type to be used for simulating the model.</p>
-<h4 id="returns-3">Returns</h4>
-<p>ematrix instance refering to the loaded model container.</p>
-<h2 id="move">move</h2>
-<p>Move a ematrix object to a destination.</p>
-<h2 id="quit">quit</h2>
-<p>Finalize MOOSE threads and quit MOOSE. This is made available for debugging purpose only. It will automatically get called when moose module is unloaded. End user should not use this function.</p>
-<h2 id="reinit">reinit</h2>
-<p>reinit() -> None</p>
-<p>Reinitialize simulation.</p>
-<p>This function (re)initializes moose simulation. It must be called</p>
-<p>before you start the simulation (see moose.start). If you want to</p>
-<p>continue simulation after you have called moose.reinit() and</p>
-<p>moose.start(), you must NOT call moose.reinit() again. Calling</p>
-<p>moose.reinit() again will take the system back to initial setting</p>
-<p>(like clear out all data recording tables, set state variables to</p>
-<p>their initial values, etc.</p>
-<h2 id="savemodel">saveModel</h2>
-<p>saveModel(source, fileame)</p>
-<p>Save model rooted at <code>source</code> to file <code>filename</code>.</p>
-<h4 id="parameters-6">Parameters</h4>
-<p>source: ematrix or element or str</p>
-<p>root of the model tree</p>
-<p>filename: str</p>
-<p>destination file to save the model in.</p>
-<h4 id="returns-4">Returns</h4>
-<p>None</p>
-<h2 id="seed">seed</h2>
-<p>moose.seed(seedvalue) -> None</p>
-<p>Reseed MOOSE random number generator.</p>
-<h4 id="parameters-7">Parameters</h4>
-<p>seed: int</p>
-<p>Optional value to use for seeding. If 0, a random seed is</p>
-<p>automatically created using the current system time and other</p>
-<p>information. If not specified, it defaults to 0.</p>
-<h2 id="setclock">setClock</h2>
-<p>Set the dt of a clock.</p>
-<h2 id="setcwe">setCwe</h2>
-<p>Set the current working element. 'ce' is an alias of this function</p>
-<h2 id="start">start</h2>
-<p>start(t) -> None</p>
-<p>Run simulation for <code>t</code> time. Advances the simulator clock by <code>t</code></p>
-<p>time.</p>
-<p>After setting up a simulation, YOU MUST CALL MOOSE.REINIT() before</p>
-<p>CALLING MOOSE.START() TO EXECUTE THE SIMULATION. Otherwise, the</p>
-<p>simulator behaviour will be undefined. Once moose.reinit() has been</p>
-<p>called, you can call moose.start(t) as many time as you like. This</p>
-<p>will continue the simulation from the last state for <code>t</code> time.</p>
-<h4 id="parameters-8">Parameters</h4>
-<p>t : float</p>
-<p>duration of simulation.</p>
-<h4 id="returns-5">Returns</h4>
-<p>None</p>
-<h4 id="see-also">See also</h4>
-<p>moose.reinit : (Re)initialize simulation</p>
-<h2 id="stop">stop</h2>
-<p>Stop simulation</p>
-<h2 id="useclock">useClock</h2>
-<p>Schedule objects on a specified clock</p>
-<h2 id="wildcardfind">wildcardFind</h2>
-<p>moose.wildcardFind(expression) -> tuple of ematrices.</p>
-<p>Find an object by wildcard.</p>
-<h4 id="parameters-9">Parameters</h4>
-<p>expression: str</p>
-<p>MOOSE allows wildcard expressions of the form</p>
-<p>{PATH}/{WILDCARD}[{CONDITION}]</p>
-<p>where {PATH} is valid path in the element tree.</p>
-<p>{WILDCARD} can be <code>#</code> or <code>##</code>.</p>
-<p><code>#</code> causes the search to be restricted to the children of the</p>
-<p>element specified by {PATH}.</p>
-<p><code>##</code> makes the search to recursively go through all the descendants</p>
-<p>of the {PATH} element.</p>
-<p>{CONDITION} can be</p>
-<p>TYPE={CLASSNAME} : an element satisfies this condition if it is of</p>
-<p>class {CLASSNAME}.</p>
-<p>ISA={CLASSNAME} : alias for TYPE={CLASSNAME}</p>
-<p>CLASS={CLASSNAME} : alias for TYPE={CLASSNAME}</p>
-<p>FIELD({FIELDNAME}){OPERATOR}{VALUE} : compare field {FIELDNAME} with</p>
-<p>{VALUE} by {OPERATOR} where {OPERATOR} is a comparison operator (=,</p>
-<p>!=, >, <, >=, <=).</p>
-<p>For example, /mymodel/##[FIELD(Vm)>=-65] will return a list of all</p>
-<p>the objects under /mymodel whose Vm field is >= -65.</p>
-<h2 id="writesbml">writeSBML</h2>
-<p>Export biochemical model to an SBML file.</p>
-<h2 id="doc">doc</h2>
-<p>Display the documentation for class or field in a class.</p>
-<h4 id="parameters-10">Parameters</h4>
-<p>arg: str or moose class or instance of melement or instance of ematrix</p>
-<p>argument can be a string specifying a moose class name and a field</p>
-<p>name separated by a dot. e.g., 'Neutral.name'. Prepending <code>moose.</code></p>
-<p>is allowed. Thus moose.doc('moose.Neutral.name') is equivalent to</p>
-<p>the above.</p>
-<p>argument can also be string specifying just a moose class name or</p>
-<p>a moose class or a moose object (instance of melement or ematrix</p>
-<p>or there subclasses). In that case, the builtin documentation for</p>
-<p>the corresponding moose class is displayed.</p>
-<p>paged: bool</p>
-<p>Whether to display the docs via builtin pager or print and</p>
-<p>exit. If not specified, it defaults to False and moose.doc(xyz)</p>
-<p>will print help on xyz and return control to command line.</p>
-<h2 id="getfielddoc">getfielddoc</h2>
-<p>Get the documentation for field specified by</p>
-<p>tokens.</p>
-<p>tokens should be a two element list/tuple where first element is a</p>
-<p>MOOSE class name and second is the field name.</p>
-<h2 id="getmoosedoc">getmoosedoc</h2>
-<p>Retrieve MOOSE builtin documentation for tokens.</p>
-<p>tokens is a list or tuple containing: (classname, [fieldname])</p>
-<h2 id="le">le</h2>
-<p>List elements.</p>
-<h4 id="parameters-11">Parameters</h4>
-<p>el: str/melement/ematrix/None</p>
-<p>The element or the path under which to look. If <code>None</code>, children</p>
-<p>of current working element are displayed.</p>
-<h2 id="listmsg">listmsg</h2>
-<p>Return a list containing the incoming and outgoing messages of</p>
-<p>the given object.</p>
-<h2 id="pwe">pwe</h2>
-<p>Print present working element. Convenience function for GENESIS</p>
-<p>users.</p>
-<h2 id="showfield">showfield</h2>
-<p>Show the fields of the element, their data types and values in</p>
-<p>human readable format. Convenience function for GENESIS users.</p>
-<p>Parameters:</p>
-<p>elem: str/melement instance</p>
-<p>Element or path of an existing element.</p>
-<p>field: str</p>
-<p>Field to be displayed. If '*', all fields are displayed.</p>
-<p>showtype: bool</p>
-<p>If True show the data type of each field.</p>
-<h2 id="showfields">showfields</h2>
-<p>Convenience function. Should be deprecated if nobody uses it.</p>
-<h2 id="showmsg">showmsg</h2>
-<p>Prints the incoming and outgoing messages of the given object.</p>
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diff --git a/moose-core/Docs/user/html/pymoose/_static/doctools.js b/moose-core/Docs/user/html/pymoose/_static/doctools.js
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- if (typeof translated == 'undefined')
- return string;
- return (typeof translated == 'string') ? translated : translated[0];
- },
-
- ngettext : function(singular, plural, n) {
- var translated = Documentation.TRANSLATIONS[singular];
- if (typeof translated == 'undefined')
- return (n == 1) ? singular : plural;
- return translated[Documentation.PLURALEXPR(n)];
- },
-
- addTranslations : function(catalog) {
- for (var key in catalog.messages)
- this.TRANSLATIONS[key] = catalog.messages[key];
- this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
- this.LOCALE = catalog.locale;
- },
-
- /**
- * add context elements like header anchor links
- */
- addContextElements : function() {
- $('div[id] > :header:first').each(function() {
- $('<a class="headerlink">\u00B6</a>').
- attr('href', '#' + this.id).
- attr('title', _('Permalink to this headline')).
- appendTo(this);
- });
- $('dt[id]').each(function() {
- $('<a class="headerlink">\u00B6</a>').
- attr('href', '#' + this.id).
- attr('title', _('Permalink to this definition')).
- appendTo(this);
- });
- },
-
- /**
- * workaround a firefox stupidity
- */
- fixFirefoxAnchorBug : function() {
- if (document.location.hash && $.browser.mozilla)
- window.setTimeout(function() {
- document.location.href += '';
- }, 10);
- },
-
- /**
- * highlight the search words provided in the url in the text
- */
- highlightSearchWords : function() {
- var params = $.getQueryParameters();
- var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
- if (terms.length) {
- var body = $('div.body');
- window.setTimeout(function() {
- $.each(terms, function() {
- body.highlightText(this.toLowerCase(), 'highlighted');
- });
- }, 10);
- $('<p class="highlight-link"><a href="javascript:Documentation.' +
- 'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
- .appendTo($('#searchbox'));
- }
- },
-
- /**
- * init the domain index toggle buttons
- */
- initIndexTable : function() {
- var togglers = $('img.toggler').click(function() {
- var src = $(this).attr('src');
- var idnum = $(this).attr('id').substr(7);
- $('tr.cg-' + idnum).toggle();
- if (src.substr(-9) == 'minus.png')
- $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
- else
- $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
- }).css('display', '');
- if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
- togglers.click();
- }
- },
-
- /**
- * helper function to hide the search marks again
- */
- hideSearchWords : function() {
- $('#searchbox .highlight-link').fadeOut(300);
- $('span.highlighted').removeClass('highlighted');
- },
-
- /**
- * make the url absolute
- */
- makeURL : function(relativeURL) {
- return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
- },
-
- /**
- * get the current relative url
- */
- getCurrentURL : function() {
- var path = document.location.pathname;
- var parts = path.split(/\//);
- $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
- if (this == '..')
- parts.pop();
- });
- var url = parts.join('/');
- return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
- }
-};
-
-// quick alias for translations
-_ = Documentation.gettext;
-
-$(document).ready(function() {
- Documentation.init();
-});
diff --git a/moose-core/Docs/user/html/pymoose/_static/down-pressed.png b/moose-core/Docs/user/html/pymoose/_static/down-pressed.png
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diff --git a/moose-core/Docs/user/html/pymoose/_static/down.png b/moose-core/Docs/user/html/pymoose/_static/down.png
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diff --git a/moose-core/Docs/user/html/pymoose/_static/file.png b/moose-core/Docs/user/html/pymoose/_static/file.png
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diff --git a/moose-core/Docs/user/html/pymoose/_static/jquery.js b/moose-core/Docs/user/html/pymoose/_static/jquery.js
deleted file mode 100644
index e2efc335e92c5ae608d55a533d11c380c651af3a..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/html/pymoose/_static/jquery.js
+++ /dev/null
@@ -1,9404 +0,0 @@
-/*!
- * jQuery JavaScript Library v1.7.2
- * http://jquery.com/
- *
- * Copyright 2011, John Resig
- * Dual licensed under the MIT or GPL Version 2 licenses.
- * http://jquery.org/license
- *
- * Includes Sizzle.js
- * http://sizzlejs.com/
- * Copyright 2011, The Dojo Foundation
- * Released under the MIT, BSD, and GPL Licenses.
- *
- * Date: Fri Jul 5 14:07:58 UTC 2013
- */
-(function( window, undefined ) {
-
-// Use the correct document accordingly with window argument (sandbox)
-var document = window.document,
- navigator = window.navigator,
- location = window.location;
-var jQuery = (function() {
-
-// Define a local copy of jQuery
-var jQuery = function( selector, context ) {
- // The jQuery object is actually just the init constructor 'enhanced'
- return new jQuery.fn.init( selector, context, rootjQuery );
- },
-
- // Map over jQuery in case of overwrite
- _jQuery = window.jQuery,
-
- // Map over the $ in case of overwrite
- _$ = window.$,
-
- // A central reference to the root jQuery(document)
- rootjQuery,
-
- // A simple way to check for HTML strings or ID strings
- // Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
- quickExpr = /^(?:[^#<]*(<[\w\W]+>)[^>]*$|#([\w\-]*)$)/,
-
- // Check if a string has a non-whitespace character in it
- rnotwhite = /\S/,
-
- // Used for trimming whitespace
- trimLeft = /^\s+/,
- trimRight = /\s+$/,
-
- // Match a standalone tag
- rsingleTag = /^<(\w+)\s*\/?>(?:<\/\1>)?$/,
-
- // JSON RegExp
- rvalidchars = /^[\],:{}\s]*$/,
- rvalidescape = /\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,
- rvalidtokens = /"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,
- rvalidbraces = /(?:^|:|,)(?:\s*\[)+/g,
-
- // Useragent RegExp
- rwebkit = /(webkit)[ \/]([\w.]+)/,
- ropera = /(opera)(?:.*version)?[ \/]([\w.]+)/,
- rmsie = /(msie) ([\w.]+)/,
- rmozilla = /(mozilla)(?:.*? rv:([\w.]+))?/,
-
- // Matches dashed string for camelizing
- rdashAlpha = /-([a-z]|[0-9])/ig,
- rmsPrefix = /^-ms-/,
-
- // Used by jQuery.camelCase as callback to replace()
- fcamelCase = function( all, letter ) {
- return ( letter + "" ).toUpperCase();
- },
-
- // Keep a UserAgent string for use with jQuery.browser
- userAgent = navigator.userAgent,
-
- // For matching the engine and version of the browser
- browserMatch,
-
- // The deferred used on DOM ready
- readyList,
-
- // The ready event handler
- DOMContentLoaded,
-
- // Save a reference to some core methods
- toString = Object.prototype.toString,
- hasOwn = Object.prototype.hasOwnProperty,
- push = Array.prototype.push,
- slice = Array.prototype.slice,
- trim = String.prototype.trim,
- indexOf = Array.prototype.indexOf,
-
- // [[Class]] -> type pairs
- class2type = {};
-
-jQuery.fn = jQuery.prototype = {
- constructor: jQuery,
- init: function( selector, context, rootjQuery ) {
- var match, elem, ret, doc;
-
- // Handle $(""), $(null), or $(undefined)
- if ( !selector ) {
- return this;
- }
-
- // Handle $(DOMElement)
- if ( selector.nodeType ) {
- this.context = this[0] = selector;
- this.length = 1;
- return this;
- }
-
- // The body element only exists once, optimize finding it
- if ( selector === "body" && !context && document.body ) {
- this.context = document;
- this[0] = document.body;
- this.selector = selector;
- this.length = 1;
- return this;
- }
-
- // Handle HTML strings
- if ( typeof selector === "string" ) {
- // Are we dealing with HTML string or an ID?
- if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) {
- // Assume that strings that start and end with <> are HTML and skip the regex check
- match = [ null, selector, null ];
-
- } else {
- match = quickExpr.exec( selector );
- }
-
- // Verify a match, and that no context was specified for #id
- if ( match && (match[1] || !context) ) {
-
- // HANDLE: $(html) -> $(array)
- if ( match[1] ) {
- context = context instanceof jQuery ? context[0] : context;
- doc = ( context ? context.ownerDocument || context : document );
-
- // If a single string is passed in and it's a single tag
- // just do a createElement and skip the rest
- ret = rsingleTag.exec( selector );
-
- if ( ret ) {
- if ( jQuery.isPlainObject( context ) ) {
- selector = [ document.createElement( ret[1] ) ];
- jQuery.fn.attr.call( selector, context, true );
-
- } else {
- selector = [ doc.createElement( ret[1] ) ];
- }
-
- } else {
- ret = jQuery.buildFragment( [ match[1] ], [ doc ] );
- selector = ( ret.cacheable ? jQuery.clone(ret.fragment) : ret.fragment ).childNodes;
- }
-
- return jQuery.merge( this, selector );
-
- // HANDLE: $("#id")
- } else {
- elem = document.getElementById( match[2] );
-
- // Check parentNode to catch when Blackberry 4.6 returns
- // nodes that are no longer in the document #6963
- if ( elem && elem.parentNode ) {
- // Handle the case where IE and Opera return items
- // by name instead of ID
- if ( elem.id !== match[2] ) {
- return rootjQuery.find( selector );
- }
-
- // Otherwise, we inject the element directly into the jQuery object
- this.length = 1;
- this[0] = elem;
- }
-
- this.context = document;
- this.selector = selector;
- return this;
- }
-
- // HANDLE: $(expr, $(...))
- } else if ( !context || context.jquery ) {
- return ( context || rootjQuery ).find( selector );
-
- // HANDLE: $(expr, context)
- // (which is just equivalent to: $(context).find(expr)
- } else {
- return this.constructor( context ).find( selector );
- }
-
- // HANDLE: $(function)
- // Shortcut for document ready
- } else if ( jQuery.isFunction( selector ) ) {
- return rootjQuery.ready( selector );
- }
-
- if ( selector.selector !== undefined ) {
- this.selector = selector.selector;
- this.context = selector.context;
- }
-
- return jQuery.makeArray( selector, this );
- },
-
- // Start with an empty selector
- selector: "",
-
- // The current version of jQuery being used
- jquery: "1.7.2",
-
- // The default length of a jQuery object is 0
- length: 0,
-
- // The number of elements contained in the matched element set
- size: function() {
- return this.length;
- },
-
- toArray: function() {
- return slice.call( this, 0 );
- },
-
- // Get the Nth element in the matched element set OR
- // Get the whole matched element set as a clean array
- get: function( num ) {
- return num == null ?
-
- // Return a 'clean' array
- this.toArray() :
-
- // Return just the object
- ( num < 0 ? this[ this.length + num ] : this[ num ] );
- },
-
- // Take an array of elements and push it onto the stack
- // (returning the new matched element set)
- pushStack: function( elems, name, selector ) {
- // Build a new jQuery matched element set
- var ret = this.constructor();
-
- if ( jQuery.isArray( elems ) ) {
- push.apply( ret, elems );
-
- } else {
- jQuery.merge( ret, elems );
- }
-
- // Add the old object onto the stack (as a reference)
- ret.prevObject = this;
-
- ret.context = this.context;
-
- if ( name === "find" ) {
- ret.selector = this.selector + ( this.selector ? " " : "" ) + selector;
- } else if ( name ) {
- ret.selector = this.selector + "." + name + "(" + selector + ")";
- }
-
- // Return the newly-formed element set
- return ret;
- },
-
- // Execute a callback for every element in the matched set.
- // (You can seed the arguments with an array of args, but this is
- // only used internally.)
- each: function( callback, args ) {
- return jQuery.each( this, callback, args );
- },
-
- ready: function( fn ) {
- // Attach the listeners
- jQuery.bindReady();
-
- // Add the callback
- readyList.add( fn );
-
- return this;
- },
-
- eq: function( i ) {
- i = +i;
- return i === -1 ?
- this.slice( i ) :
- this.slice( i, i + 1 );
- },
-
- first: function() {
- return this.eq( 0 );
- },
-
- last: function() {
- return this.eq( -1 );
- },
-
- slice: function() {
- return this.pushStack( slice.apply( this, arguments ),
- "slice", slice.call(arguments).join(",") );
- },
-
- map: function( callback ) {
- return this.pushStack( jQuery.map(this, function( elem, i ) {
- return callback.call( elem, i, elem );
- }));
- },
-
- end: function() {
- return this.prevObject || this.constructor(null);
- },
-
- // For internal use only.
- // Behaves like an Array's method, not like a jQuery method.
- push: push,
- sort: [].sort,
- splice: [].splice
-};
-
-// Give the init function the jQuery prototype for later instantiation
-jQuery.fn.init.prototype = jQuery.fn;
-
-jQuery.extend = jQuery.fn.extend = function() {
- var options, name, src, copy, copyIsArray, clone,
- target = arguments[0] || {},
- i = 1,
- length = arguments.length,
- deep = false;
-
- // Handle a deep copy situation
- if ( typeof target === "boolean" ) {
- deep = target;
- target = arguments[1] || {};
- // skip the boolean and the target
- i = 2;
- }
-
- // Handle case when target is a string or something (possible in deep copy)
- if ( typeof target !== "object" && !jQuery.isFunction(target) ) {
- target = {};
- }
-
- // extend jQuery itself if only one argument is passed
- if ( length === i ) {
- target = this;
- --i;
- }
-
- for ( ; i < length; i++ ) {
- // Only deal with non-null/undefined values
- if ( (options = arguments[ i ]) != null ) {
- // Extend the base object
- for ( name in options ) {
- src = target[ name ];
- copy = options[ name ];
-
- // Prevent never-ending loop
- if ( target === copy ) {
- continue;
- }
-
- // Recurse if we're merging plain objects or arrays
- if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) {
- if ( copyIsArray ) {
- copyIsArray = false;
- clone = src && jQuery.isArray(src) ? src : [];
-
- } else {
- clone = src && jQuery.isPlainObject(src) ? src : {};
- }
-
- // Never move original objects, clone them
- target[ name ] = jQuery.extend( deep, clone, copy );
-
- // Don't bring in undefined values
- } else if ( copy !== undefined ) {
- target[ name ] = copy;
- }
- }
- }
- }
-
- // Return the modified object
- return target;
-};
-
-jQuery.extend({
- noConflict: function( deep ) {
- if ( window.$ === jQuery ) {
- window.$ = _$;
- }
-
- if ( deep && window.jQuery === jQuery ) {
- window.jQuery = _jQuery;
- }
-
- return jQuery;
- },
-
- // Is the DOM ready to be used? Set to true once it occurs.
- isReady: false,
-
- // A counter to track how many items to wait for before
- // the ready event fires. See #6781
- readyWait: 1,
-
- // Hold (or release) the ready event
- holdReady: function( hold ) {
- if ( hold ) {
- jQuery.readyWait++;
- } else {
- jQuery.ready( true );
- }
- },
-
- // Handle when the DOM is ready
- ready: function( wait ) {
- // Either a released hold or an DOMready/load event and not yet ready
- if ( (wait === true && !--jQuery.readyWait) || (wait !== true && !jQuery.isReady) ) {
- // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
- if ( !document.body ) {
- return setTimeout( jQuery.ready, 1 );
- }
-
- // Remember that the DOM is ready
- jQuery.isReady = true;
-
- // If a normal DOM Ready event fired, decrement, and wait if need be
- if ( wait !== true && --jQuery.readyWait > 0 ) {
- return;
- }
-
- // If there are functions bound, to execute
- readyList.fireWith( document, [ jQuery ] );
-
- // Trigger any bound ready events
- if ( jQuery.fn.trigger ) {
- jQuery( document ).trigger( "ready" ).off( "ready" );
- }
- }
- },
-
- bindReady: function() {
- if ( readyList ) {
- return;
- }
-
- readyList = jQuery.Callbacks( "once memory" );
-
- // Catch cases where $(document).ready() is called after the
- // browser event has already occurred.
- if ( document.readyState === "complete" ) {
- // Handle it asynchronously to allow scripts the opportunity to delay ready
- return setTimeout( jQuery.ready, 1 );
- }
-
- // Mozilla, Opera and webkit nightlies currently support this event
- if ( document.addEventListener ) {
- // Use the handy event callback
- document.addEventListener( "DOMContentLoaded", DOMContentLoaded, false );
-
- // A fallback to window.onload, that will always work
- window.addEventListener( "load", jQuery.ready, false );
-
- // If IE event model is used
- } else if ( document.attachEvent ) {
- // ensure firing before onload,
- // maybe late but safe also for iframes
- document.attachEvent( "onreadystatechange", DOMContentLoaded );
-
- // A fallback to window.onload, that will always work
- window.attachEvent( "onload", jQuery.ready );
-
- // If IE and not a frame
- // continually check to see if the document is ready
- var toplevel = false;
-
- try {
- toplevel = window.frameElement == null;
- } catch(e) {}
-
- if ( document.documentElement.doScroll && toplevel ) {
- doScrollCheck();
- }
- }
- },
-
- // See test/unit/core.js for details concerning isFunction.
- // Since version 1.3, DOM methods and functions like alert
- // aren't supported. They return false on IE (#2968).
- isFunction: function( obj ) {
- return jQuery.type(obj) === "function";
- },
-
- isArray: Array.isArray || function( obj ) {
- return jQuery.type(obj) === "array";
- },
-
- isWindow: function( obj ) {
- return obj != null && obj == obj.window;
- },
-
- isNumeric: function( obj ) {
- return !isNaN( parseFloat(obj) ) && isFinite( obj );
- },
-
- type: function( obj ) {
- return obj == null ?
- String( obj ) :
- class2type[ toString.call(obj) ] || "object";
- },
-
- isPlainObject: function( obj ) {
- // Must be an Object.
- // Because of IE, we also have to check the presence of the constructor property.
- // Make sure that DOM nodes and window objects don't pass through, as well
- if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) {
- return false;
- }
-
- try {
- // Not own constructor property must be Object
- if ( obj.constructor &&
- !hasOwn.call(obj, "constructor") &&
- !hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) {
- return false;
- }
- } catch ( e ) {
- // IE8,9 Will throw exceptions on certain host objects #9897
- return false;
- }
-
- // Own properties are enumerated firstly, so to speed up,
- // if last one is own, then all properties are own.
-
- var key;
- for ( key in obj ) {}
-
- return key === undefined || hasOwn.call( obj, key );
- },
-
- isEmptyObject: function( obj ) {
- for ( var name in obj ) {
- return false;
- }
- return true;
- },
-
- error: function( msg ) {
- throw new Error( msg );
- },
-
- parseJSON: function( data ) {
- if ( typeof data !== "string" || !data ) {
- return null;
- }
-
- // Make sure leading/trailing whitespace is removed (IE can't handle it)
- data = jQuery.trim( data );
-
- // Attempt to parse using the native JSON parser first
- if ( window.JSON && window.JSON.parse ) {
- return window.JSON.parse( data );
- }
-
- // Make sure the incoming data is actual JSON
- // Logic borrowed from http://json.org/json2.js
- if ( rvalidchars.test( data.replace( rvalidescape, "@" )
- .replace( rvalidtokens, "]" )
- .replace( rvalidbraces, "")) ) {
-
- return ( new Function( "return " + data ) )();
-
- }
- jQuery.error( "Invalid JSON: " + data );
- },
-
- // Cross-browser xml parsing
- parseXML: function( data ) {
- if ( typeof data !== "string" || !data ) {
- return null;
- }
- var xml, tmp;
- try {
- if ( window.DOMParser ) { // Standard
- tmp = new DOMParser();
- xml = tmp.parseFromString( data , "text/xml" );
- } else { // IE
- xml = new ActiveXObject( "Microsoft.XMLDOM" );
- xml.async = "false";
- xml.loadXML( data );
- }
- } catch( e ) {
- xml = undefined;
- }
- if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) {
- jQuery.error( "Invalid XML: " + data );
- }
- return xml;
- },
-
- noop: function() {},
-
- // Evaluates a script in a global context
- // Workarounds based on findings by Jim Driscoll
- // http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context
- globalEval: function( data ) {
- if ( data && rnotwhite.test( data ) ) {
- // We use execScript on Internet Explorer
- // We use an anonymous function so that context is window
- // rather than jQuery in Firefox
- ( window.execScript || function( data ) {
- window[ "eval" ].call( window, data );
- } )( data );
- }
- },
-
- // Convert dashed to camelCase; used by the css and data modules
- // Microsoft forgot to hump their vendor prefix (#9572)
- camelCase: function( string ) {
- return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
- },
-
- nodeName: function( elem, name ) {
- return elem.nodeName && elem.nodeName.toUpperCase() === name.toUpperCase();
- },
-
- // args is for internal usage only
- each: function( object, callback, args ) {
- var name, i = 0,
- length = object.length,
- isObj = length === undefined || jQuery.isFunction( object );
-
- if ( args ) {
- if ( isObj ) {
- for ( name in object ) {
- if ( callback.apply( object[ name ], args ) === false ) {
- break;
- }
- }
- } else {
- for ( ; i < length; ) {
- if ( callback.apply( object[ i++ ], args ) === false ) {
- break;
- }
- }
- }
-
- // A special, fast, case for the most common use of each
- } else {
- if ( isObj ) {
- for ( name in object ) {
- if ( callback.call( object[ name ], name, object[ name ] ) === false ) {
- break;
- }
- }
- } else {
- for ( ; i < length; ) {
- if ( callback.call( object[ i ], i, object[ i++ ] ) === false ) {
- break;
- }
- }
- }
- }
-
- return object;
- },
-
- // Use native String.trim function wherever possible
- trim: trim ?
- function( text ) {
- return text == null ?
- "" :
- trim.call( text );
- } :
-
- // Otherwise use our own trimming functionality
- function( text ) {
- return text == null ?
- "" :
- text.toString().replace( trimLeft, "" ).replace( trimRight, "" );
- },
-
- // results is for internal usage only
- makeArray: function( array, results ) {
- var ret = results || [];
-
- if ( array != null ) {
- // The window, strings (and functions) also have 'length'
- // Tweaked logic slightly to handle Blackberry 4.7 RegExp issues #6930
- var type = jQuery.type( array );
-
- if ( array.length == null || type === "string" || type === "function" || type === "regexp" || jQuery.isWindow( array ) ) {
- push.call( ret, array );
- } else {
- jQuery.merge( ret, array );
- }
- }
-
- return ret;
- },
-
- inArray: function( elem, array, i ) {
- var len;
-
- if ( array ) {
- if ( indexOf ) {
- return indexOf.call( array, elem, i );
- }
-
- len = array.length;
- i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0;
-
- for ( ; i < len; i++ ) {
- // Skip accessing in sparse arrays
- if ( i in array && array[ i ] === elem ) {
- return i;
- }
- }
- }
-
- return -1;
- },
-
- merge: function( first, second ) {
- var i = first.length,
- j = 0;
-
- if ( typeof second.length === "number" ) {
- for ( var l = second.length; j < l; j++ ) {
- first[ i++ ] = second[ j ];
- }
-
- } else {
- while ( second[j] !== undefined ) {
- first[ i++ ] = second[ j++ ];
- }
- }
-
- first.length = i;
-
- return first;
- },
-
- grep: function( elems, callback, inv ) {
- var ret = [], retVal;
- inv = !!inv;
-
- // Go through the array, only saving the items
- // that pass the validator function
- for ( var i = 0, length = elems.length; i < length; i++ ) {
- retVal = !!callback( elems[ i ], i );
- if ( inv !== retVal ) {
- ret.push( elems[ i ] );
- }
- }
-
- return ret;
- },
-
- // arg is for internal usage only
- map: function( elems, callback, arg ) {
- var value, key, ret = [],
- i = 0,
- length = elems.length,
- // jquery objects are treated as arrays
- isArray = elems instanceof jQuery || length !== undefined && typeof length === "number" && ( ( length > 0 && elems[ 0 ] && elems[ length -1 ] ) || length === 0 || jQuery.isArray( elems ) ) ;
-
- // Go through the array, translating each of the items to their
- if ( isArray ) {
- for ( ; i < length; i++ ) {
- value = callback( elems[ i ], i, arg );
-
- if ( value != null ) {
- ret[ ret.length ] = value;
- }
- }
-
- // Go through every key on the object,
- } else {
- for ( key in elems ) {
- value = callback( elems[ key ], key, arg );
-
- if ( value != null ) {
- ret[ ret.length ] = value;
- }
- }
- }
-
- // Flatten any nested arrays
- return ret.concat.apply( [], ret );
- },
-
- // A global GUID counter for objects
- guid: 1,
-
- // Bind a function to a context, optionally partially applying any
- // arguments.
- proxy: function( fn, context ) {
- if ( typeof context === "string" ) {
- var tmp = fn[ context ];
- context = fn;
- fn = tmp;
- }
-
- // Quick check to determine if target is callable, in the spec
- // this throws a TypeError, but we will just return undefined.
- if ( !jQuery.isFunction( fn ) ) {
- return undefined;
- }
-
- // Simulated bind
- var args = slice.call( arguments, 2 ),
- proxy = function() {
- return fn.apply( context, args.concat( slice.call( arguments ) ) );
- };
-
- // Set the guid of unique handler to the same of original handler, so it can be removed
- proxy.guid = fn.guid = fn.guid || proxy.guid || jQuery.guid++;
-
- return proxy;
- },
-
- // Mutifunctional method to get and set values to a collection
- // The value/s can optionally be executed if it's a function
- access: function( elems, fn, key, value, chainable, emptyGet, pass ) {
- var exec,
- bulk = key == null,
- i = 0,
- length = elems.length;
-
- // Sets many values
- if ( key && typeof key === "object" ) {
- for ( i in key ) {
- jQuery.access( elems, fn, i, key[i], 1, emptyGet, value );
- }
- chainable = 1;
-
- // Sets one value
- } else if ( value !== undefined ) {
- // Optionally, function values get executed if exec is true
- exec = pass === undefined && jQuery.isFunction( value );
-
- if ( bulk ) {
- // Bulk operations only iterate when executing function values
- if ( exec ) {
- exec = fn;
- fn = function( elem, key, value ) {
- return exec.call( jQuery( elem ), value );
- };
-
- // Otherwise they run against the entire set
- } else {
- fn.call( elems, value );
- fn = null;
- }
- }
-
- if ( fn ) {
- for (; i < length; i++ ) {
- fn( elems[i], key, exec ? value.call( elems[i], i, fn( elems[i], key ) ) : value, pass );
- }
- }
-
- chainable = 1;
- }
-
- return chainable ?
- elems :
-
- // Gets
- bulk ?
- fn.call( elems ) :
- length ? fn( elems[0], key ) : emptyGet;
- },
-
- now: function() {
- return ( new Date() ).getTime();
- },
-
- // Use of jQuery.browser is frowned upon.
- // More details: http://docs.jquery.com/Utilities/jQuery.browser
- uaMatch: function( ua ) {
- ua = ua.toLowerCase();
-
- var match = rwebkit.exec( ua ) ||
- ropera.exec( ua ) ||
- rmsie.exec( ua ) ||
- ua.indexOf("compatible") < 0 && rmozilla.exec( ua ) ||
- [];
-
- return { browser: match[1] || "", version: match[2] || "0" };
- },
-
- sub: function() {
- function jQuerySub( selector, context ) {
- return new jQuerySub.fn.init( selector, context );
- }
- jQuery.extend( true, jQuerySub, this );
- jQuerySub.superclass = this;
- jQuerySub.fn = jQuerySub.prototype = this();
- jQuerySub.fn.constructor = jQuerySub;
- jQuerySub.sub = this.sub;
- jQuerySub.fn.init = function init( selector, context ) {
- if ( context && context instanceof jQuery && !(context instanceof jQuerySub) ) {
- context = jQuerySub( context );
- }
-
- return jQuery.fn.init.call( this, selector, context, rootjQuerySub );
- };
- jQuerySub.fn.init.prototype = jQuerySub.fn;
- var rootjQuerySub = jQuerySub(document);
- return jQuerySub;
- },
-
- browser: {}
-});
-
-// Populate the class2type map
-jQuery.each("Boolean Number String Function Array Date RegExp Object".split(" "), function(i, name) {
- class2type[ "[object " + name + "]" ] = name.toLowerCase();
-});
-
-browserMatch = jQuery.uaMatch( userAgent );
-if ( browserMatch.browser ) {
- jQuery.browser[ browserMatch.browser ] = true;
- jQuery.browser.version = browserMatch.version;
-}
-
-// Deprecated, use jQuery.browser.webkit instead
-if ( jQuery.browser.webkit ) {
- jQuery.browser.safari = true;
-}
-
-// IE doesn't match non-breaking spaces with \s
-if ( rnotwhite.test( "\xA0" ) ) {
- trimLeft = /^[\s\xA0]+/;
- trimRight = /[\s\xA0]+$/;
-}
-
-// All jQuery objects should point back to these
-rootjQuery = jQuery(document);
-
-// Cleanup functions for the document ready method
-if ( document.addEventListener ) {
- DOMContentLoaded = function() {
- document.removeEventListener( "DOMContentLoaded", DOMContentLoaded, false );
- jQuery.ready();
- };
-
-} else if ( document.attachEvent ) {
- DOMContentLoaded = function() {
- // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
- if ( document.readyState === "complete" ) {
- document.detachEvent( "onreadystatechange", DOMContentLoaded );
- jQuery.ready();
- }
- };
-}
-
-// The DOM ready check for Internet Explorer
-function doScrollCheck() {
- if ( jQuery.isReady ) {
- return;
- }
-
- try {
- // If IE is used, use the trick by Diego Perini
- // http://javascript.nwbox.com/IEContentLoaded/
- document.documentElement.doScroll("left");
- } catch(e) {
- setTimeout( doScrollCheck, 1 );
- return;
- }
-
- // and execute any waiting functions
- jQuery.ready();
-}
-
-return jQuery;
-
-})();
-
-
-// String to Object flags format cache
-var flagsCache = {};
-
-// Convert String-formatted flags into Object-formatted ones and store in cache
-function createFlags( flags ) {
- var object = flagsCache[ flags ] = {},
- i, length;
- flags = flags.split( /\s+/ );
- for ( i = 0, length = flags.length; i < length; i++ ) {
- object[ flags[i] ] = true;
- }
- return object;
-}
-
-/*
- * Create a callback list using the following parameters:
- *
- * flags: an optional list of space-separated flags that will change how
- * the callback list behaves
- *
- * By default a callback list will act like an event callback list and can be
- * "fired" multiple times.
- *
- * Possible flags:
- *
- * once: will ensure the callback list can only be fired once (like a Deferred)
- *
- * memory: will keep track of previous values and will call any callback added
- * after the list has been fired right away with the latest "memorized"
- * values (like a Deferred)
- *
- * unique: will ensure a callback can only be added once (no duplicate in the list)
- *
- * stopOnFalse: interrupt callings when a callback returns false
- *
- */
-jQuery.Callbacks = function( flags ) {
-
- // Convert flags from String-formatted to Object-formatted
- // (we check in cache first)
- flags = flags ? ( flagsCache[ flags ] || createFlags( flags ) ) : {};
-
- var // Actual callback list
- list = [],
- // Stack of fire calls for repeatable lists
- stack = [],
- // Last fire value (for non-forgettable lists)
- memory,
- // Flag to know if list was already fired
- fired,
- // Flag to know if list is currently firing
- firing,
- // First callback to fire (used internally by add and fireWith)
- firingStart,
- // End of the loop when firing
- firingLength,
- // Index of currently firing callback (modified by remove if needed)
- firingIndex,
- // Add one or several callbacks to the list
- add = function( args ) {
- var i,
- length,
- elem,
- type,
- actual;
- for ( i = 0, length = args.length; i < length; i++ ) {
- elem = args[ i ];
- type = jQuery.type( elem );
- if ( type === "array" ) {
- // Inspect recursively
- add( elem );
- } else if ( type === "function" ) {
- // Add if not in unique mode and callback is not in
- if ( !flags.unique || !self.has( elem ) ) {
- list.push( elem );
- }
- }
- }
- },
- // Fire callbacks
- fire = function( context, args ) {
- args = args || [];
- memory = !flags.memory || [ context, args ];
- fired = true;
- firing = true;
- firingIndex = firingStart || 0;
- firingStart = 0;
- firingLength = list.length;
- for ( ; list && firingIndex < firingLength; firingIndex++ ) {
- if ( list[ firingIndex ].apply( context, args ) === false && flags.stopOnFalse ) {
- memory = true; // Mark as halted
- break;
- }
- }
- firing = false;
- if ( list ) {
- if ( !flags.once ) {
- if ( stack && stack.length ) {
- memory = stack.shift();
- self.fireWith( memory[ 0 ], memory[ 1 ] );
- }
- } else if ( memory === true ) {
- self.disable();
- } else {
- list = [];
- }
- }
- },
- // Actual Callbacks object
- self = {
- // Add a callback or a collection of callbacks to the list
- add: function() {
- if ( list ) {
- var length = list.length;
- add( arguments );
- // Do we need to add the callbacks to the
- // current firing batch?
- if ( firing ) {
- firingLength = list.length;
- // With memory, if we're not firing then
- // we should call right away, unless previous
- // firing was halted (stopOnFalse)
- } else if ( memory && memory !== true ) {
- firingStart = length;
- fire( memory[ 0 ], memory[ 1 ] );
- }
- }
- return this;
- },
- // Remove a callback from the list
- remove: function() {
- if ( list ) {
- var args = arguments,
- argIndex = 0,
- argLength = args.length;
- for ( ; argIndex < argLength ; argIndex++ ) {
- for ( var i = 0; i < list.length; i++ ) {
- if ( args[ argIndex ] === list[ i ] ) {
- // Handle firingIndex and firingLength
- if ( firing ) {
- if ( i <= firingLength ) {
- firingLength--;
- if ( i <= firingIndex ) {
- firingIndex--;
- }
- }
- }
- // Remove the element
- list.splice( i--, 1 );
- // If we have some unicity property then
- // we only need to do this once
- if ( flags.unique ) {
- break;
- }
- }
- }
- }
- }
- return this;
- },
- // Control if a given callback is in the list
- has: function( fn ) {
- if ( list ) {
- var i = 0,
- length = list.length;
- for ( ; i < length; i++ ) {
- if ( fn === list[ i ] ) {
- return true;
- }
- }
- }
- return false;
- },
- // Remove all callbacks from the list
- empty: function() {
- list = [];
- return this;
- },
- // Have the list do nothing anymore
- disable: function() {
- list = stack = memory = undefined;
- return this;
- },
- // Is it disabled?
- disabled: function() {
- return !list;
- },
- // Lock the list in its current state
- lock: function() {
- stack = undefined;
- if ( !memory || memory === true ) {
- self.disable();
- }
- return this;
- },
- // Is it locked?
- locked: function() {
- return !stack;
- },
- // Call all callbacks with the given context and arguments
- fireWith: function( context, args ) {
- if ( stack ) {
- if ( firing ) {
- if ( !flags.once ) {
- stack.push( [ context, args ] );
- }
- } else if ( !( flags.once && memory ) ) {
- fire( context, args );
- }
- }
- return this;
- },
- // Call all the callbacks with the given arguments
- fire: function() {
- self.fireWith( this, arguments );
- return this;
- },
- // To know if the callbacks have already been called at least once
- fired: function() {
- return !!fired;
- }
- };
-
- return self;
-};
-
-
-
-
-var // Static reference to slice
- sliceDeferred = [].slice;
-
-jQuery.extend({
-
- Deferred: function( func ) {
- var doneList = jQuery.Callbacks( "once memory" ),
- failList = jQuery.Callbacks( "once memory" ),
- progressList = jQuery.Callbacks( "memory" ),
- state = "pending",
- lists = {
- resolve: doneList,
- reject: failList,
- notify: progressList
- },
- promise = {
- done: doneList.add,
- fail: failList.add,
- progress: progressList.add,
-
- state: function() {
- return state;
- },
-
- // Deprecated
- isResolved: doneList.fired,
- isRejected: failList.fired,
-
- then: function( doneCallbacks, failCallbacks, progressCallbacks ) {
- deferred.done( doneCallbacks ).fail( failCallbacks ).progress( progressCallbacks );
- return this;
- },
- always: function() {
- deferred.done.apply( deferred, arguments ).fail.apply( deferred, arguments );
- return this;
- },
- pipe: function( fnDone, fnFail, fnProgress ) {
- return jQuery.Deferred(function( newDefer ) {
- jQuery.each( {
- done: [ fnDone, "resolve" ],
- fail: [ fnFail, "reject" ],
- progress: [ fnProgress, "notify" ]
- }, function( handler, data ) {
- var fn = data[ 0 ],
- action = data[ 1 ],
- returned;
- if ( jQuery.isFunction( fn ) ) {
- deferred[ handler ](function() {
- returned = fn.apply( this, arguments );
- if ( returned && jQuery.isFunction( returned.promise ) ) {
- returned.promise().then( newDefer.resolve, newDefer.reject, newDefer.notify );
- } else {
- newDefer[ action + "With" ]( this === deferred ? newDefer : this, [ returned ] );
- }
- });
- } else {
- deferred[ handler ]( newDefer[ action ] );
- }
- });
- }).promise();
- },
- // Get a promise for this deferred
- // If obj is provided, the promise aspect is added to the object
- promise: function( obj ) {
- if ( obj == null ) {
- obj = promise;
- } else {
- for ( var key in promise ) {
- obj[ key ] = promise[ key ];
- }
- }
- return obj;
- }
- },
- deferred = promise.promise({}),
- key;
-
- for ( key in lists ) {
- deferred[ key ] = lists[ key ].fire;
- deferred[ key + "With" ] = lists[ key ].fireWith;
- }
-
- // Handle state
- deferred.done( function() {
- state = "resolved";
- }, failList.disable, progressList.lock ).fail( function() {
- state = "rejected";
- }, doneList.disable, progressList.lock );
-
- // Call given func if any
- if ( func ) {
- func.call( deferred, deferred );
- }
-
- // All done!
- return deferred;
- },
-
- // Deferred helper
- when: function( firstParam ) {
- var args = sliceDeferred.call( arguments, 0 ),
- i = 0,
- length = args.length,
- pValues = new Array( length ),
- count = length,
- pCount = length,
- deferred = length <= 1 && firstParam && jQuery.isFunction( firstParam.promise ) ?
- firstParam :
- jQuery.Deferred(),
- promise = deferred.promise();
- function resolveFunc( i ) {
- return function( value ) {
- args[ i ] = arguments.length > 1 ? sliceDeferred.call( arguments, 0 ) : value;
- if ( !( --count ) ) {
- deferred.resolveWith( deferred, args );
- }
- };
- }
- function progressFunc( i ) {
- return function( value ) {
- pValues[ i ] = arguments.length > 1 ? sliceDeferred.call( arguments, 0 ) : value;
- deferred.notifyWith( promise, pValues );
- };
- }
- if ( length > 1 ) {
- for ( ; i < length; i++ ) {
- if ( args[ i ] && args[ i ].promise && jQuery.isFunction( args[ i ].promise ) ) {
- args[ i ].promise().then( resolveFunc(i), deferred.reject, progressFunc(i) );
- } else {
- --count;
- }
- }
- if ( !count ) {
- deferred.resolveWith( deferred, args );
- }
- } else if ( deferred !== firstParam ) {
- deferred.resolveWith( deferred, length ? [ firstParam ] : [] );
- }
- return promise;
- }
-});
-
-
-
-
-jQuery.support = (function() {
-
- var support,
- all,
- a,
- select,
- opt,
- input,
- fragment,
- tds,
- events,
- eventName,
- i,
- isSupported,
- div = document.createElement( "div" ),
- documentElement = document.documentElement;
-
- // Preliminary tests
- div.setAttribute("className", "t");
- div.innerHTML = " <link/><table></table><a href='/a' style='top:1px;float:left;opacity:.55;'>a</a><input type='checkbox'/>";
-
- all = div.getElementsByTagName( "*" );
- a = div.getElementsByTagName( "a" )[ 0 ];
-
- // Can't get basic test support
- if ( !all || !all.length || !a ) {
- return {};
- }
-
- // First batch of supports tests
- select = document.createElement( "select" );
- opt = select.appendChild( document.createElement("option") );
- input = div.getElementsByTagName( "input" )[ 0 ];
-
- support = {
- // IE strips leading whitespace when .innerHTML is used
- leadingWhitespace: ( div.firstChild.nodeType === 3 ),
-
- // Make sure that tbody elements aren't automatically inserted
- // IE will insert them into empty tables
- tbody: !div.getElementsByTagName("tbody").length,
-
- // Make sure that link elements get serialized correctly by innerHTML
- // This requires a wrapper element in IE
- htmlSerialize: !!div.getElementsByTagName("link").length,
-
- // Get the style information from getAttribute
- // (IE uses .cssText instead)
- style: /top/.test( a.getAttribute("style") ),
-
- // Make sure that URLs aren't manipulated
- // (IE normalizes it by default)
- hrefNormalized: ( a.getAttribute("href") === "/a" ),
-
- // Make sure that element opacity exists
- // (IE uses filter instead)
- // Use a regex to work around a WebKit issue. See #5145
- opacity: /^0.55/.test( a.style.opacity ),
-
- // Verify style float existence
- // (IE uses styleFloat instead of cssFloat)
- cssFloat: !!a.style.cssFloat,
-
- // Make sure that if no value is specified for a checkbox
- // that it defaults to "on".
- // (WebKit defaults to "" instead)
- checkOn: ( input.value === "on" ),
-
- // Make sure that a selected-by-default option has a working selected property.
- // (WebKit defaults to false instead of true, IE too, if it's in an optgroup)
- optSelected: opt.selected,
-
- // Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7)
- getSetAttribute: div.className !== "t",
-
- // Tests for enctype support on a form(#6743)
- enctype: !!document.createElement("form").enctype,
-
- // Makes sure cloning an html5 element does not cause problems
- // Where outerHTML is undefined, this still works
- html5Clone: document.createElement("nav").cloneNode( true ).outerHTML !== "<:nav></:nav>",
-
- // Will be defined later
- submitBubbles: true,
- changeBubbles: true,
- focusinBubbles: false,
- deleteExpando: true,
- noCloneEvent: true,
- inlineBlockNeedsLayout: false,
- shrinkWrapBlocks: false,
- reliableMarginRight: true,
- pixelMargin: true
- };
-
- // jQuery.boxModel DEPRECATED in 1.3, use jQuery.support.boxModel instead
- jQuery.boxModel = support.boxModel = (document.compatMode === "CSS1Compat");
-
- // Make sure checked status is properly cloned
- input.checked = true;
- support.noCloneChecked = input.cloneNode( true ).checked;
-
- // Make sure that the options inside disabled selects aren't marked as disabled
- // (WebKit marks them as disabled)
- select.disabled = true;
- support.optDisabled = !opt.disabled;
-
- // Test to see if it's possible to delete an expando from an element
- // Fails in Internet Explorer
- try {
- delete div.test;
- } catch( e ) {
- support.deleteExpando = false;
- }
-
- if ( !div.addEventListener && div.attachEvent && div.fireEvent ) {
- div.attachEvent( "onclick", function() {
- // Cloning a node shouldn't copy over any
- // bound event handlers (IE does this)
- support.noCloneEvent = false;
- });
- div.cloneNode( true ).fireEvent( "onclick" );
- }
-
- // Check if a radio maintains its value
- // after being appended to the DOM
- input = document.createElement("input");
- input.value = "t";
- input.setAttribute("type", "radio");
- support.radioValue = input.value === "t";
-
- input.setAttribute("checked", "checked");
-
- // #11217 - WebKit loses check when the name is after the checked attribute
- input.setAttribute( "name", "t" );
-
- div.appendChild( input );
- fragment = document.createDocumentFragment();
- fragment.appendChild( div.lastChild );
-
- // WebKit doesn't clone checked state correctly in fragments
- support.checkClone = fragment.cloneNode( true ).cloneNode( true ).lastChild.checked;
-
- // Check if a disconnected checkbox will retain its checked
- // value of true after appended to the DOM (IE6/7)
- support.appendChecked = input.checked;
-
- fragment.removeChild( input );
- fragment.appendChild( div );
-
- // Technique from Juriy Zaytsev
- // http://perfectionkills.com/detecting-event-support-without-browser-sniffing/
- // We only care about the case where non-standard event systems
- // are used, namely in IE. Short-circuiting here helps us to
- // avoid an eval call (in setAttribute) which can cause CSP
- // to go haywire. See: https://developer.mozilla.org/en/Security/CSP
- if ( div.attachEvent ) {
- for ( i in {
- submit: 1,
- change: 1,
- focusin: 1
- }) {
- eventName = "on" + i;
- isSupported = ( eventName in div );
- if ( !isSupported ) {
- div.setAttribute( eventName, "return;" );
- isSupported = ( typeof div[ eventName ] === "function" );
- }
- support[ i + "Bubbles" ] = isSupported;
- }
- }
-
- fragment.removeChild( div );
-
- // Null elements to avoid leaks in IE
- fragment = select = opt = div = input = null;
-
- // Run tests that need a body at doc ready
- jQuery(function() {
- var container, outer, inner, table, td, offsetSupport,
- marginDiv, conMarginTop, style, html, positionTopLeftWidthHeight,
- paddingMarginBorderVisibility, paddingMarginBorder,
- body = document.getElementsByTagName("body")[0];
-
- if ( !body ) {
- // Return for frameset docs that don't have a body
- return;
- }
-
- conMarginTop = 1;
- paddingMarginBorder = "padding:0;margin:0;border:";
- positionTopLeftWidthHeight = "position:absolute;top:0;left:0;width:1px;height:1px;";
- paddingMarginBorderVisibility = paddingMarginBorder + "0;visibility:hidden;";
- style = "style='" + positionTopLeftWidthHeight + paddingMarginBorder + "5px solid #000;";
- html = "<div " + style + "display:block;'><div style='" + paddingMarginBorder + "0;display:block;overflow:hidden;'></div></div>" +
- "<table " + style + "' cellpadding='0' cellspacing='0'>" +
- "<tr><td></td></tr></table>";
-
- container = document.createElement("div");
- container.style.cssText = paddingMarginBorderVisibility + "width:0;height:0;position:static;top:0;margin-top:" + conMarginTop + "px";
- body.insertBefore( container, body.firstChild );
-
- // Construct the test element
- div = document.createElement("div");
- container.appendChild( div );
-
- // Check if table cells still have offsetWidth/Height when they are set
- // to display:none and there are still other visible table cells in a
- // table row; if so, offsetWidth/Height are not reliable for use when
- // determining if an element has been hidden directly using
- // display:none (it is still safe to use offsets if a parent element is
- // hidden; don safety goggles and see bug #4512 for more information).
- // (only IE 8 fails this test)
- div.innerHTML = "<table><tr><td style='" + paddingMarginBorder + "0;display:none'></td><td>t</td></tr></table>";
- tds = div.getElementsByTagName( "td" );
- isSupported = ( tds[ 0 ].offsetHeight === 0 );
-
- tds[ 0 ].style.display = "";
- tds[ 1 ].style.display = "none";
-
- // Check if empty table cells still have offsetWidth/Height
- // (IE <= 8 fail this test)
- support.reliableHiddenOffsets = isSupported && ( tds[ 0 ].offsetHeight === 0 );
-
- // Check if div with explicit width and no margin-right incorrectly
- // gets computed margin-right based on width of container. For more
- // info see bug #3333
- // Fails in WebKit before Feb 2011 nightlies
- // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
- if ( window.getComputedStyle ) {
- div.innerHTML = "";
- marginDiv = document.createElement( "div" );
- marginDiv.style.width = "0";
- marginDiv.style.marginRight = "0";
- div.style.width = "2px";
- div.appendChild( marginDiv );
- support.reliableMarginRight =
- ( parseInt( ( window.getComputedStyle( marginDiv, null ) || { marginRight: 0 } ).marginRight, 10 ) || 0 ) === 0;
- }
-
- if ( typeof div.style.zoom !== "undefined" ) {
- // Check if natively block-level elements act like inline-block
- // elements when setting their display to 'inline' and giving
- // them layout
- // (IE < 8 does this)
- div.innerHTML = "";
- div.style.width = div.style.padding = "1px";
- div.style.border = 0;
- div.style.overflow = "hidden";
- div.style.display = "inline";
- div.style.zoom = 1;
- support.inlineBlockNeedsLayout = ( div.offsetWidth === 3 );
-
- // Check if elements with layout shrink-wrap their children
- // (IE 6 does this)
- div.style.display = "block";
- div.style.overflow = "visible";
- div.innerHTML = "<div style='width:5px;'></div>";
- support.shrinkWrapBlocks = ( div.offsetWidth !== 3 );
- }
-
- div.style.cssText = positionTopLeftWidthHeight + paddingMarginBorderVisibility;
- div.innerHTML = html;
-
- outer = div.firstChild;
- inner = outer.firstChild;
- td = outer.nextSibling.firstChild.firstChild;
-
- offsetSupport = {
- doesNotAddBorder: ( inner.offsetTop !== 5 ),
- doesAddBorderForTableAndCells: ( td.offsetTop === 5 )
- };
-
- inner.style.position = "fixed";
- inner.style.top = "20px";
-
- // safari subtracts parent border width here which is 5px
- offsetSupport.fixedPosition = ( inner.offsetTop === 20 || inner.offsetTop === 15 );
- inner.style.position = inner.style.top = "";
-
- outer.style.overflow = "hidden";
- outer.style.position = "relative";
-
- offsetSupport.subtractsBorderForOverflowNotVisible = ( inner.offsetTop === -5 );
- offsetSupport.doesNotIncludeMarginInBodyOffset = ( body.offsetTop !== conMarginTop );
-
- if ( window.getComputedStyle ) {
- div.style.marginTop = "1%";
- support.pixelMargin = ( window.getComputedStyle( div, null ) || { marginTop: 0 } ).marginTop !== "1%";
- }
-
- if ( typeof container.style.zoom !== "undefined" ) {
- container.style.zoom = 1;
- }
-
- body.removeChild( container );
- marginDiv = div = container = null;
-
- jQuery.extend( support, offsetSupport );
- });
-
- return support;
-})();
-
-
-
-
-var rbrace = /^(?:\{.*\}|\[.*\])$/,
- rmultiDash = /([A-Z])/g;
-
-jQuery.extend({
- cache: {},
-
- // Please use with caution
- uuid: 0,
-
- // Unique for each copy of jQuery on the page
- // Non-digits removed to match rinlinejQuery
- expando: "jQuery" + ( jQuery.fn.jquery + Math.random() ).replace( /\D/g, "" ),
-
- // The following elements throw uncatchable exceptions if you
- // attempt to add expando properties to them.
- noData: {
- "embed": true,
- // Ban all objects except for Flash (which handle expandos)
- "object": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000",
- "applet": true
- },
-
- hasData: function( elem ) {
- elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ];
- return !!elem && !isEmptyDataObject( elem );
- },
-
- data: function( elem, name, data, pvt /* Internal Use Only */ ) {
- if ( !jQuery.acceptData( elem ) ) {
- return;
- }
-
- var privateCache, thisCache, ret,
- internalKey = jQuery.expando,
- getByName = typeof name === "string",
-
- // We have to handle DOM nodes and JS objects differently because IE6-7
- // can't GC object references properly across the DOM-JS boundary
- isNode = elem.nodeType,
-
- // Only DOM nodes need the global jQuery cache; JS object data is
- // attached directly to the object so GC can occur automatically
- cache = isNode ? jQuery.cache : elem,
-
- // Only defining an ID for JS objects if its cache already exists allows
- // the code to shortcut on the same path as a DOM node with no cache
- id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey,
- isEvents = name === "events";
-
- // Avoid doing any more work than we need to when trying to get data on an
- // object that has no data at all
- if ( (!id || !cache[id] || (!isEvents && !pvt && !cache[id].data)) && getByName && data === undefined ) {
- return;
- }
-
- if ( !id ) {
- // Only DOM nodes need a new unique ID for each element since their data
- // ends up in the global cache
- if ( isNode ) {
- elem[ internalKey ] = id = ++jQuery.uuid;
- } else {
- id = internalKey;
- }
- }
-
- if ( !cache[ id ] ) {
- cache[ id ] = {};
-
- // Avoids exposing jQuery metadata on plain JS objects when the object
- // is serialized using JSON.stringify
- if ( !isNode ) {
- cache[ id ].toJSON = jQuery.noop;
- }
- }
-
- // An object can be passed to jQuery.data instead of a key/value pair; this gets
- // shallow copied over onto the existing cache
- if ( typeof name === "object" || typeof name === "function" ) {
- if ( pvt ) {
- cache[ id ] = jQuery.extend( cache[ id ], name );
- } else {
- cache[ id ].data = jQuery.extend( cache[ id ].data, name );
- }
- }
-
- privateCache = thisCache = cache[ id ];
-
- // jQuery data() is stored in a separate object inside the object's internal data
- // cache in order to avoid key collisions between internal data and user-defined
- // data.
- if ( !pvt ) {
- if ( !thisCache.data ) {
- thisCache.data = {};
- }
-
- thisCache = thisCache.data;
- }
-
- if ( data !== undefined ) {
- thisCache[ jQuery.camelCase( name ) ] = data;
- }
-
- // Users should not attempt to inspect the internal events object using jQuery.data,
- // it is undocumented and subject to change. But does anyone listen? No.
- if ( isEvents && !thisCache[ name ] ) {
- return privateCache.events;
- }
-
- // Check for both converted-to-camel and non-converted data property names
- // If a data property was specified
- if ( getByName ) {
-
- // First Try to find as-is property data
- ret = thisCache[ name ];
-
- // Test for null|undefined property data
- if ( ret == null ) {
-
- // Try to find the camelCased property
- ret = thisCache[ jQuery.camelCase( name ) ];
- }
- } else {
- ret = thisCache;
- }
-
- return ret;
- },
-
- removeData: function( elem, name, pvt /* Internal Use Only */ ) {
- if ( !jQuery.acceptData( elem ) ) {
- return;
- }
-
- var thisCache, i, l,
-
- // Reference to internal data cache key
- internalKey = jQuery.expando,
-
- isNode = elem.nodeType,
-
- // See jQuery.data for more information
- cache = isNode ? jQuery.cache : elem,
-
- // See jQuery.data for more information
- id = isNode ? elem[ internalKey ] : internalKey;
-
- // If there is already no cache entry for this object, there is no
- // purpose in continuing
- if ( !cache[ id ] ) {
- return;
- }
-
- if ( name ) {
-
- thisCache = pvt ? cache[ id ] : cache[ id ].data;
-
- if ( thisCache ) {
-
- // Support array or space separated string names for data keys
- if ( !jQuery.isArray( name ) ) {
-
- // try the string as a key before any manipulation
- if ( name in thisCache ) {
- name = [ name ];
- } else {
-
- // split the camel cased version by spaces unless a key with the spaces exists
- name = jQuery.camelCase( name );
- if ( name in thisCache ) {
- name = [ name ];
- } else {
- name = name.split( " " );
- }
- }
- }
-
- for ( i = 0, l = name.length; i < l; i++ ) {
- delete thisCache[ name[i] ];
- }
-
- // If there is no data left in the cache, we want to continue
- // and let the cache object itself get destroyed
- if ( !( pvt ? isEmptyDataObject : jQuery.isEmptyObject )( thisCache ) ) {
- return;
- }
- }
- }
-
- // See jQuery.data for more information
- if ( !pvt ) {
- delete cache[ id ].data;
-
- // Don't destroy the parent cache unless the internal data object
- // had been the only thing left in it
- if ( !isEmptyDataObject(cache[ id ]) ) {
- return;
- }
- }
-
- // Browsers that fail expando deletion also refuse to delete expandos on
- // the window, but it will allow it on all other JS objects; other browsers
- // don't care
- // Ensure that `cache` is not a window object #10080
- if ( jQuery.support.deleteExpando || !cache.setInterval ) {
- delete cache[ id ];
- } else {
- cache[ id ] = null;
- }
-
- // We destroyed the cache and need to eliminate the expando on the node to avoid
- // false lookups in the cache for entries that no longer exist
- if ( isNode ) {
- // IE does not allow us to delete expando properties from nodes,
- // nor does it have a removeAttribute function on Document nodes;
- // we must handle all of these cases
- if ( jQuery.support.deleteExpando ) {
- delete elem[ internalKey ];
- } else if ( elem.removeAttribute ) {
- elem.removeAttribute( internalKey );
- } else {
- elem[ internalKey ] = null;
- }
- }
- },
-
- // For internal use only.
- _data: function( elem, name, data ) {
- return jQuery.data( elem, name, data, true );
- },
-
- // A method for determining if a DOM node can handle the data expando
- acceptData: function( elem ) {
- if ( elem.nodeName ) {
- var match = jQuery.noData[ elem.nodeName.toLowerCase() ];
-
- if ( match ) {
- return !(match === true || elem.getAttribute("classid") !== match);
- }
- }
-
- return true;
- }
-});
-
-jQuery.fn.extend({
- data: function( key, value ) {
- var parts, part, attr, name, l,
- elem = this[0],
- i = 0,
- data = null;
-
- // Gets all values
- if ( key === undefined ) {
- if ( this.length ) {
- data = jQuery.data( elem );
-
- if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) {
- attr = elem.attributes;
- for ( l = attr.length; i < l; i++ ) {
- name = attr[i].name;
-
- if ( name.indexOf( "data-" ) === 0 ) {
- name = jQuery.camelCase( name.substring(5) );
-
- dataAttr( elem, name, data[ name ] );
- }
- }
- jQuery._data( elem, "parsedAttrs", true );
- }
- }
-
- return data;
- }
-
- // Sets multiple values
- if ( typeof key === "object" ) {
- return this.each(function() {
- jQuery.data( this, key );
- });
- }
-
- parts = key.split( ".", 2 );
- parts[1] = parts[1] ? "." + parts[1] : "";
- part = parts[1] + "!";
-
- return jQuery.access( this, function( value ) {
-
- if ( value === undefined ) {
- data = this.triggerHandler( "getData" + part, [ parts[0] ] );
-
- // Try to fetch any internally stored data first
- if ( data === undefined && elem ) {
- data = jQuery.data( elem, key );
- data = dataAttr( elem, key, data );
- }
-
- return data === undefined && parts[1] ?
- this.data( parts[0] ) :
- data;
- }
-
- parts[1] = value;
- this.each(function() {
- var self = jQuery( this );
-
- self.triggerHandler( "setData" + part, parts );
- jQuery.data( this, key, value );
- self.triggerHandler( "changeData" + part, parts );
- });
- }, null, value, arguments.length > 1, null, false );
- },
-
- removeData: function( key ) {
- return this.each(function() {
- jQuery.removeData( this, key );
- });
- }
-});
-
-function dataAttr( elem, key, data ) {
- // If nothing was found internally, try to fetch any
- // data from the HTML5 data-* attribute
- if ( data === undefined && elem.nodeType === 1 ) {
-
- var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase();
-
- data = elem.getAttribute( name );
-
- if ( typeof data === "string" ) {
- try {
- data = data === "true" ? true :
- data === "false" ? false :
- data === "null" ? null :
- jQuery.isNumeric( data ) ? +data :
- rbrace.test( data ) ? jQuery.parseJSON( data ) :
- data;
- } catch( e ) {}
-
- // Make sure we set the data so it isn't changed later
- jQuery.data( elem, key, data );
-
- } else {
- data = undefined;
- }
- }
-
- return data;
-}
-
-// checks a cache object for emptiness
-function isEmptyDataObject( obj ) {
- for ( var name in obj ) {
-
- // if the public data object is empty, the private is still empty
- if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) {
- continue;
- }
- if ( name !== "toJSON" ) {
- return false;
- }
- }
-
- return true;
-}
-
-
-
-
-function handleQueueMarkDefer( elem, type, src ) {
- var deferDataKey = type + "defer",
- queueDataKey = type + "queue",
- markDataKey = type + "mark",
- defer = jQuery._data( elem, deferDataKey );
- if ( defer &&
- ( src === "queue" || !jQuery._data(elem, queueDataKey) ) &&
- ( src === "mark" || !jQuery._data(elem, markDataKey) ) ) {
- // Give room for hard-coded callbacks to fire first
- // and eventually mark/queue something else on the element
- setTimeout( function() {
- if ( !jQuery._data( elem, queueDataKey ) &&
- !jQuery._data( elem, markDataKey ) ) {
- jQuery.removeData( elem, deferDataKey, true );
- defer.fire();
- }
- }, 0 );
- }
-}
-
-jQuery.extend({
-
- _mark: function( elem, type ) {
- if ( elem ) {
- type = ( type || "fx" ) + "mark";
- jQuery._data( elem, type, (jQuery._data( elem, type ) || 0) + 1 );
- }
- },
-
- _unmark: function( force, elem, type ) {
- if ( force !== true ) {
- type = elem;
- elem = force;
- force = false;
- }
- if ( elem ) {
- type = type || "fx";
- var key = type + "mark",
- count = force ? 0 : ( (jQuery._data( elem, key ) || 1) - 1 );
- if ( count ) {
- jQuery._data( elem, key, count );
- } else {
- jQuery.removeData( elem, key, true );
- handleQueueMarkDefer( elem, type, "mark" );
- }
- }
- },
-
- queue: function( elem, type, data ) {
- var q;
- if ( elem ) {
- type = ( type || "fx" ) + "queue";
- q = jQuery._data( elem, type );
-
- // Speed up dequeue by getting out quickly if this is just a lookup
- if ( data ) {
- if ( !q || jQuery.isArray(data) ) {
- q = jQuery._data( elem, type, jQuery.makeArray(data) );
- } else {
- q.push( data );
- }
- }
- return q || [];
- }
- },
-
- dequeue: function( elem, type ) {
- type = type || "fx";
-
- var queue = jQuery.queue( elem, type ),
- fn = queue.shift(),
- hooks = {};
-
- // If the fx queue is dequeued, always remove the progress sentinel
- if ( fn === "inprogress" ) {
- fn = queue.shift();
- }
-
- if ( fn ) {
- // Add a progress sentinel to prevent the fx queue from being
- // automatically dequeued
- if ( type === "fx" ) {
- queue.unshift( "inprogress" );
- }
-
- jQuery._data( elem, type + ".run", hooks );
- fn.call( elem, function() {
- jQuery.dequeue( elem, type );
- }, hooks );
- }
-
- if ( !queue.length ) {
- jQuery.removeData( elem, type + "queue " + type + ".run", true );
- handleQueueMarkDefer( elem, type, "queue" );
- }
- }
-});
-
-jQuery.fn.extend({
- queue: function( type, data ) {
- var setter = 2;
-
- if ( typeof type !== "string" ) {
- data = type;
- type = "fx";
- setter--;
- }
-
- if ( arguments.length < setter ) {
- return jQuery.queue( this[0], type );
- }
-
- return data === undefined ?
- this :
- this.each(function() {
- var queue = jQuery.queue( this, type, data );
-
- if ( type === "fx" && queue[0] !== "inprogress" ) {
- jQuery.dequeue( this, type );
- }
- });
- },
- dequeue: function( type ) {
- return this.each(function() {
- jQuery.dequeue( this, type );
- });
- },
- // Based off of the plugin by Clint Helfers, with permission.
- // http://blindsignals.com/index.php/2009/07/jquery-delay/
- delay: function( time, type ) {
- time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
- type = type || "fx";
-
- return this.queue( type, function( next, hooks ) {
- var timeout = setTimeout( next, time );
- hooks.stop = function() {
- clearTimeout( timeout );
- };
- });
- },
- clearQueue: function( type ) {
- return this.queue( type || "fx", [] );
- },
- // Get a promise resolved when queues of a certain type
- // are emptied (fx is the type by default)
- promise: function( type, object ) {
- if ( typeof type !== "string" ) {
- object = type;
- type = undefined;
- }
- type = type || "fx";
- var defer = jQuery.Deferred(),
- elements = this,
- i = elements.length,
- count = 1,
- deferDataKey = type + "defer",
- queueDataKey = type + "queue",
- markDataKey = type + "mark",
- tmp;
- function resolve() {
- if ( !( --count ) ) {
- defer.resolveWith( elements, [ elements ] );
- }
- }
- while( i-- ) {
- if (( tmp = jQuery.data( elements[ i ], deferDataKey, undefined, true ) ||
- ( jQuery.data( elements[ i ], queueDataKey, undefined, true ) ||
- jQuery.data( elements[ i ], markDataKey, undefined, true ) ) &&
- jQuery.data( elements[ i ], deferDataKey, jQuery.Callbacks( "once memory" ), true ) )) {
- count++;
- tmp.add( resolve );
- }
- }
- resolve();
- return defer.promise( object );
- }
-});
-
-
-
-
-var rclass = /[\n\t\r]/g,
- rspace = /\s+/,
- rreturn = /\r/g,
- rtype = /^(?:button|input)$/i,
- rfocusable = /^(?:button|input|object|select|textarea)$/i,
- rclickable = /^a(?:rea)?$/i,
- rboolean = /^(?:autofocus|autoplay|async|checked|controls|defer|disabled|hidden|loop|multiple|open|readonly|required|scoped|selected)$/i,
- getSetAttribute = jQuery.support.getSetAttribute,
- nodeHook, boolHook, fixSpecified;
-
-jQuery.fn.extend({
- attr: function( name, value ) {
- return jQuery.access( this, jQuery.attr, name, value, arguments.length > 1 );
- },
-
- removeAttr: function( name ) {
- return this.each(function() {
- jQuery.removeAttr( this, name );
- });
- },
-
- prop: function( name, value ) {
- return jQuery.access( this, jQuery.prop, name, value, arguments.length > 1 );
- },
-
- removeProp: function( name ) {
- name = jQuery.propFix[ name ] || name;
- return this.each(function() {
- // try/catch handles cases where IE balks (such as removing a property on window)
- try {
- this[ name ] = undefined;
- delete this[ name ];
- } catch( e ) {}
- });
- },
-
- addClass: function( value ) {
- var classNames, i, l, elem,
- setClass, c, cl;
-
- if ( jQuery.isFunction( value ) ) {
- return this.each(function( j ) {
- jQuery( this ).addClass( value.call(this, j, this.className) );
- });
- }
-
- if ( value && typeof value === "string" ) {
- classNames = value.split( rspace );
-
- for ( i = 0, l = this.length; i < l; i++ ) {
- elem = this[ i ];
-
- if ( elem.nodeType === 1 ) {
- if ( !elem.className && classNames.length === 1 ) {
- elem.className = value;
-
- } else {
- setClass = " " + elem.className + " ";
-
- for ( c = 0, cl = classNames.length; c < cl; c++ ) {
- if ( !~setClass.indexOf( " " + classNames[ c ] + " " ) ) {
- setClass += classNames[ c ] + " ";
- }
- }
- elem.className = jQuery.trim( setClass );
- }
- }
- }
- }
-
- return this;
- },
-
- removeClass: function( value ) {
- var classNames, i, l, elem, className, c, cl;
-
- if ( jQuery.isFunction( value ) ) {
- return this.each(function( j ) {
- jQuery( this ).removeClass( value.call(this, j, this.className) );
- });
- }
-
- if ( (value && typeof value === "string") || value === undefined ) {
- classNames = ( value || "" ).split( rspace );
-
- for ( i = 0, l = this.length; i < l; i++ ) {
- elem = this[ i ];
-
- if ( elem.nodeType === 1 && elem.className ) {
- if ( value ) {
- className = (" " + elem.className + " ").replace( rclass, " " );
- for ( c = 0, cl = classNames.length; c < cl; c++ ) {
- className = className.replace(" " + classNames[ c ] + " ", " ");
- }
- elem.className = jQuery.trim( className );
-
- } else {
- elem.className = "";
- }
- }
- }
- }
-
- return this;
- },
-
- toggleClass: function( value, stateVal ) {
- var type = typeof value,
- isBool = typeof stateVal === "boolean";
-
- if ( jQuery.isFunction( value ) ) {
- return this.each(function( i ) {
- jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal );
- });
- }
-
- return this.each(function() {
- if ( type === "string" ) {
- // toggle individual class names
- var className,
- i = 0,
- self = jQuery( this ),
- state = stateVal,
- classNames = value.split( rspace );
-
- while ( (className = classNames[ i++ ]) ) {
- // check each className given, space seperated list
- state = isBool ? state : !self.hasClass( className );
- self[ state ? "addClass" : "removeClass" ]( className );
- }
-
- } else if ( type === "undefined" || type === "boolean" ) {
- if ( this.className ) {
- // store className if set
- jQuery._data( this, "__className__", this.className );
- }
-
- // toggle whole className
- this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || "";
- }
- });
- },
-
- hasClass: function( selector ) {
- var className = " " + selector + " ",
- i = 0,
- l = this.length;
- for ( ; i < l; i++ ) {
- if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) > -1 ) {
- return true;
- }
- }
-
- return false;
- },
-
- val: function( value ) {
- var hooks, ret, isFunction,
- elem = this[0];
-
- if ( !arguments.length ) {
- if ( elem ) {
- hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ];
-
- if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) {
- return ret;
- }
-
- ret = elem.value;
-
- return typeof ret === "string" ?
- // handle most common string cases
- ret.replace(rreturn, "") :
- // handle cases where value is null/undef or number
- ret == null ? "" : ret;
- }
-
- return;
- }
-
- isFunction = jQuery.isFunction( value );
-
- return this.each(function( i ) {
- var self = jQuery(this), val;
-
- if ( this.nodeType !== 1 ) {
- return;
- }
-
- if ( isFunction ) {
- val = value.call( this, i, self.val() );
- } else {
- val = value;
- }
-
- // Treat null/undefined as ""; convert numbers to string
- if ( val == null ) {
- val = "";
- } else if ( typeof val === "number" ) {
- val += "";
- } else if ( jQuery.isArray( val ) ) {
- val = jQuery.map(val, function ( value ) {
- return value == null ? "" : value + "";
- });
- }
-
- hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
-
- // If set returns undefined, fall back to normal setting
- if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) {
- this.value = val;
- }
- });
- }
-});
-
-jQuery.extend({
- valHooks: {
- option: {
- get: function( elem ) {
- // attributes.value is undefined in Blackberry 4.7 but
- // uses .value. See #6932
- var val = elem.attributes.value;
- return !val || val.specified ? elem.value : elem.text;
- }
- },
- select: {
- get: function( elem ) {
- var value, i, max, option,
- index = elem.selectedIndex,
- values = [],
- options = elem.options,
- one = elem.type === "select-one";
-
- // Nothing was selected
- if ( index < 0 ) {
- return null;
- }
-
- // Loop through all the selected options
- i = one ? index : 0;
- max = one ? index + 1 : options.length;
- for ( ; i < max; i++ ) {
- option = options[ i ];
-
- // Don't return options that are disabled or in a disabled optgroup
- if ( option.selected && (jQuery.support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null) &&
- (!option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" )) ) {
-
- // Get the specific value for the option
- value = jQuery( option ).val();
-
- // We don't need an array for one selects
- if ( one ) {
- return value;
- }
-
- // Multi-Selects return an array
- values.push( value );
- }
- }
-
- // Fixes Bug #2551 -- select.val() broken in IE after form.reset()
- if ( one && !values.length && options.length ) {
- return jQuery( options[ index ] ).val();
- }
-
- return values;
- },
-
- set: function( elem, value ) {
- var values = jQuery.makeArray( value );
-
- jQuery(elem).find("option").each(function() {
- this.selected = jQuery.inArray( jQuery(this).val(), values ) >= 0;
- });
-
- if ( !values.length ) {
- elem.selectedIndex = -1;
- }
- return values;
- }
- }
- },
-
- attrFn: {
- val: true,
- css: true,
- html: true,
- text: true,
- data: true,
- width: true,
- height: true,
- offset: true
- },
-
- attr: function( elem, name, value, pass ) {
- var ret, hooks, notxml,
- nType = elem.nodeType;
-
- // don't get/set attributes on text, comment and attribute nodes
- if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
- return;
- }
-
- if ( pass && name in jQuery.attrFn ) {
- return jQuery( elem )[ name ]( value );
- }
-
- // Fallback to prop when attributes are not supported
- if ( typeof elem.getAttribute === "undefined" ) {
- return jQuery.prop( elem, name, value );
- }
-
- notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
-
- // All attributes are lowercase
- // Grab necessary hook if one is defined
- if ( notxml ) {
- name = name.toLowerCase();
- hooks = jQuery.attrHooks[ name ] || ( rboolean.test( name ) ? boolHook : nodeHook );
- }
-
- if ( value !== undefined ) {
-
- if ( value === null ) {
- jQuery.removeAttr( elem, name );
- return;
-
- } else if ( hooks && "set" in hooks && notxml && (ret = hooks.set( elem, value, name )) !== undefined ) {
- return ret;
-
- } else {
- elem.setAttribute( name, "" + value );
- return value;
- }
-
- } else if ( hooks && "get" in hooks && notxml && (ret = hooks.get( elem, name )) !== null ) {
- return ret;
-
- } else {
-
- ret = elem.getAttribute( name );
-
- // Non-existent attributes return null, we normalize to undefined
- return ret === null ?
- undefined :
- ret;
- }
- },
-
- removeAttr: function( elem, value ) {
- var propName, attrNames, name, l, isBool,
- i = 0;
-
- if ( value && elem.nodeType === 1 ) {
- attrNames = value.toLowerCase().split( rspace );
- l = attrNames.length;
-
- for ( ; i < l; i++ ) {
- name = attrNames[ i ];
-
- if ( name ) {
- propName = jQuery.propFix[ name ] || name;
- isBool = rboolean.test( name );
-
- // See #9699 for explanation of this approach (setting first, then removal)
- // Do not do this for boolean attributes (see #10870)
- if ( !isBool ) {
- jQuery.attr( elem, name, "" );
- }
- elem.removeAttribute( getSetAttribute ? name : propName );
-
- // Set corresponding property to false for boolean attributes
- if ( isBool && propName in elem ) {
- elem[ propName ] = false;
- }
- }
- }
- }
- },
-
- attrHooks: {
- type: {
- set: function( elem, value ) {
- // We can't allow the type property to be changed (since it causes problems in IE)
- if ( rtype.test( elem.nodeName ) && elem.parentNode ) {
- jQuery.error( "type property can't be changed" );
- } else if ( !jQuery.support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) {
- // Setting the type on a radio button after the value resets the value in IE6-9
- // Reset value to it's default in case type is set after value
- // This is for element creation
- var val = elem.value;
- elem.setAttribute( "type", value );
- if ( val ) {
- elem.value = val;
- }
- return value;
- }
- }
- },
- // Use the value property for back compat
- // Use the nodeHook for button elements in IE6/7 (#1954)
- value: {
- get: function( elem, name ) {
- if ( nodeHook && jQuery.nodeName( elem, "button" ) ) {
- return nodeHook.get( elem, name );
- }
- return name in elem ?
- elem.value :
- null;
- },
- set: function( elem, value, name ) {
- if ( nodeHook && jQuery.nodeName( elem, "button" ) ) {
- return nodeHook.set( elem, value, name );
- }
- // Does not return so that setAttribute is also used
- elem.value = value;
- }
- }
- },
-
- propFix: {
- tabindex: "tabIndex",
- readonly: "readOnly",
- "for": "htmlFor",
- "class": "className",
- maxlength: "maxLength",
- cellspacing: "cellSpacing",
- cellpadding: "cellPadding",
- rowspan: "rowSpan",
- colspan: "colSpan",
- usemap: "useMap",
- frameborder: "frameBorder",
- contenteditable: "contentEditable"
- },
-
- prop: function( elem, name, value ) {
- var ret, hooks, notxml,
- nType = elem.nodeType;
-
- // don't get/set properties on text, comment and attribute nodes
- if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
- return;
- }
-
- notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
-
- if ( notxml ) {
- // Fix name and attach hooks
- name = jQuery.propFix[ name ] || name;
- hooks = jQuery.propHooks[ name ];
- }
-
- if ( value !== undefined ) {
- if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) {
- return ret;
-
- } else {
- return ( elem[ name ] = value );
- }
-
- } else {
- if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) {
- return ret;
-
- } else {
- return elem[ name ];
- }
- }
- },
-
- propHooks: {
- tabIndex: {
- get: function( elem ) {
- // elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set
- // http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
- var attributeNode = elem.getAttributeNode("tabindex");
-
- return attributeNode && attributeNode.specified ?
- parseInt( attributeNode.value, 10 ) :
- rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ?
- 0 :
- undefined;
- }
- }
- }
-});
-
-// Add the tabIndex propHook to attrHooks for back-compat (different case is intentional)
-jQuery.attrHooks.tabindex = jQuery.propHooks.tabIndex;
-
-// Hook for boolean attributes
-boolHook = {
- get: function( elem, name ) {
- // Align boolean attributes with corresponding properties
- // Fall back to attribute presence where some booleans are not supported
- var attrNode,
- property = jQuery.prop( elem, name );
- return property === true || typeof property !== "boolean" && ( attrNode = elem.getAttributeNode(name) ) && attrNode.nodeValue !== false ?
- name.toLowerCase() :
- undefined;
- },
- set: function( elem, value, name ) {
- var propName;
- if ( value === false ) {
- // Remove boolean attributes when set to false
- jQuery.removeAttr( elem, name );
- } else {
- // value is true since we know at this point it's type boolean and not false
- // Set boolean attributes to the same name and set the DOM property
- propName = jQuery.propFix[ name ] || name;
- if ( propName in elem ) {
- // Only set the IDL specifically if it already exists on the element
- elem[ propName ] = true;
- }
-
- elem.setAttribute( name, name.toLowerCase() );
- }
- return name;
- }
-};
-
-// IE6/7 do not support getting/setting some attributes with get/setAttribute
-if ( !getSetAttribute ) {
-
- fixSpecified = {
- name: true,
- id: true,
- coords: true
- };
-
- // Use this for any attribute in IE6/7
- // This fixes almost every IE6/7 issue
- nodeHook = jQuery.valHooks.button = {
- get: function( elem, name ) {
- var ret;
- ret = elem.getAttributeNode( name );
- return ret && ( fixSpecified[ name ] ? ret.nodeValue !== "" : ret.specified ) ?
- ret.nodeValue :
- undefined;
- },
- set: function( elem, value, name ) {
- // Set the existing or create a new attribute node
- var ret = elem.getAttributeNode( name );
- if ( !ret ) {
- ret = document.createAttribute( name );
- elem.setAttributeNode( ret );
- }
- return ( ret.nodeValue = value + "" );
- }
- };
-
- // Apply the nodeHook to tabindex
- jQuery.attrHooks.tabindex.set = nodeHook.set;
-
- // Set width and height to auto instead of 0 on empty string( Bug #8150 )
- // This is for removals
- jQuery.each([ "width", "height" ], function( i, name ) {
- jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], {
- set: function( elem, value ) {
- if ( value === "" ) {
- elem.setAttribute( name, "auto" );
- return value;
- }
- }
- });
- });
-
- // Set contenteditable to false on removals(#10429)
- // Setting to empty string throws an error as an invalid value
- jQuery.attrHooks.contenteditable = {
- get: nodeHook.get,
- set: function( elem, value, name ) {
- if ( value === "" ) {
- value = "false";
- }
- nodeHook.set( elem, value, name );
- }
- };
-}
-
-
-// Some attributes require a special call on IE
-if ( !jQuery.support.hrefNormalized ) {
- jQuery.each([ "href", "src", "width", "height" ], function( i, name ) {
- jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], {
- get: function( elem ) {
- var ret = elem.getAttribute( name, 2 );
- return ret === null ? undefined : ret;
- }
- });
- });
-}
-
-if ( !jQuery.support.style ) {
- jQuery.attrHooks.style = {
- get: function( elem ) {
- // Return undefined in the case of empty string
- // Normalize to lowercase since IE uppercases css property names
- return elem.style.cssText.toLowerCase() || undefined;
- },
- set: function( elem, value ) {
- return ( elem.style.cssText = "" + value );
- }
- };
-}
-
-// Safari mis-reports the default selected property of an option
-// Accessing the parent's selectedIndex property fixes it
-if ( !jQuery.support.optSelected ) {
- jQuery.propHooks.selected = jQuery.extend( jQuery.propHooks.selected, {
- get: function( elem ) {
- var parent = elem.parentNode;
-
- if ( parent ) {
- parent.selectedIndex;
-
- // Make sure that it also works with optgroups, see #5701
- if ( parent.parentNode ) {
- parent.parentNode.selectedIndex;
- }
- }
- return null;
- }
- });
-}
-
-// IE6/7 call enctype encoding
-if ( !jQuery.support.enctype ) {
- jQuery.propFix.enctype = "encoding";
-}
-
-// Radios and checkboxes getter/setter
-if ( !jQuery.support.checkOn ) {
- jQuery.each([ "radio", "checkbox" ], function() {
- jQuery.valHooks[ this ] = {
- get: function( elem ) {
- // Handle the case where in Webkit "" is returned instead of "on" if a value isn't specified
- return elem.getAttribute("value") === null ? "on" : elem.value;
- }
- };
- });
-}
-jQuery.each([ "radio", "checkbox" ], function() {
- jQuery.valHooks[ this ] = jQuery.extend( jQuery.valHooks[ this ], {
- set: function( elem, value ) {
- if ( jQuery.isArray( value ) ) {
- return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 );
- }
- }
- });
-});
-
-
-
-
-var rformElems = /^(?:textarea|input|select)$/i,
- rtypenamespace = /^([^\.]*)?(?:\.(.+))?$/,
- rhoverHack = /(?:^|\s)hover(\.\S+)?\b/,
- rkeyEvent = /^key/,
- rmouseEvent = /^(?:mouse|contextmenu)|click/,
- rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
- rquickIs = /^(\w*)(?:#([\w\-]+))?(?:\.([\w\-]+))?$/,
- quickParse = function( selector ) {
- var quick = rquickIs.exec( selector );
- if ( quick ) {
- // 0 1 2 3
- // [ _, tag, id, class ]
- quick[1] = ( quick[1] || "" ).toLowerCase();
- quick[3] = quick[3] && new RegExp( "(?:^|\\s)" + quick[3] + "(?:\\s|$)" );
- }
- return quick;
- },
- quickIs = function( elem, m ) {
- var attrs = elem.attributes || {};
- return (
- (!m[1] || elem.nodeName.toLowerCase() === m[1]) &&
- (!m[2] || (attrs.id || {}).value === m[2]) &&
- (!m[3] || m[3].test( (attrs[ "class" ] || {}).value ))
- );
- },
- hoverHack = function( events ) {
- return jQuery.event.special.hover ? events : events.replace( rhoverHack, "mouseenter$1 mouseleave$1" );
- };
-
-/*
- * Helper functions for managing events -- not part of the public interface.
- * Props to Dean Edwards' addEvent library for many of the ideas.
- */
-jQuery.event = {
-
- add: function( elem, types, handler, data, selector ) {
-
- var elemData, eventHandle, events,
- t, tns, type, namespaces, handleObj,
- handleObjIn, quick, handlers, special;
-
- // Don't attach events to noData or text/comment nodes (allow plain objects tho)
- if ( elem.nodeType === 3 || elem.nodeType === 8 || !types || !handler || !(elemData = jQuery._data( elem )) ) {
- return;
- }
-
- // Caller can pass in an object of custom data in lieu of the handler
- if ( handler.handler ) {
- handleObjIn = handler;
- handler = handleObjIn.handler;
- selector = handleObjIn.selector;
- }
-
- // Make sure that the handler has a unique ID, used to find/remove it later
- if ( !handler.guid ) {
- handler.guid = jQuery.guid++;
- }
-
- // Init the element's event structure and main handler, if this is the first
- events = elemData.events;
- if ( !events ) {
- elemData.events = events = {};
- }
- eventHandle = elemData.handle;
- if ( !eventHandle ) {
- elemData.handle = eventHandle = function( e ) {
- // Discard the second event of a jQuery.event.trigger() and
- // when an event is called after a page has unloaded
- return typeof jQuery !== "undefined" && (!e || jQuery.event.triggered !== e.type) ?
- jQuery.event.dispatch.apply( eventHandle.elem, arguments ) :
- undefined;
- };
- // Add elem as a property of the handle fn to prevent a memory leak with IE non-native events
- eventHandle.elem = elem;
- }
-
- // Handle multiple events separated by a space
- // jQuery(...).bind("mouseover mouseout", fn);
- types = jQuery.trim( hoverHack(types) ).split( " " );
- for ( t = 0; t < types.length; t++ ) {
-
- tns = rtypenamespace.exec( types[t] ) || [];
- type = tns[1];
- namespaces = ( tns[2] || "" ).split( "." ).sort();
-
- // If event changes its type, use the special event handlers for the changed type
- special = jQuery.event.special[ type ] || {};
-
- // If selector defined, determine special event api type, otherwise given type
- type = ( selector ? special.delegateType : special.bindType ) || type;
-
- // Update special based on newly reset type
- special = jQuery.event.special[ type ] || {};
-
- // handleObj is passed to all event handlers
- handleObj = jQuery.extend({
- type: type,
- origType: tns[1],
- data: data,
- handler: handler,
- guid: handler.guid,
- selector: selector,
- quick: selector && quickParse( selector ),
- namespace: namespaces.join(".")
- }, handleObjIn );
-
- // Init the event handler queue if we're the first
- handlers = events[ type ];
- if ( !handlers ) {
- handlers = events[ type ] = [];
- handlers.delegateCount = 0;
-
- // Only use addEventListener/attachEvent if the special events handler returns false
- if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
- // Bind the global event handler to the element
- if ( elem.addEventListener ) {
- elem.addEventListener( type, eventHandle, false );
-
- } else if ( elem.attachEvent ) {
- elem.attachEvent( "on" + type, eventHandle );
- }
- }
- }
-
- if ( special.add ) {
- special.add.call( elem, handleObj );
-
- if ( !handleObj.handler.guid ) {
- handleObj.handler.guid = handler.guid;
- }
- }
-
- // Add to the element's handler list, delegates in front
- if ( selector ) {
- handlers.splice( handlers.delegateCount++, 0, handleObj );
- } else {
- handlers.push( handleObj );
- }
-
- // Keep track of which events have ever been used, for event optimization
- jQuery.event.global[ type ] = true;
- }
-
- // Nullify elem to prevent memory leaks in IE
- elem = null;
- },
-
- global: {},
-
- // Detach an event or set of events from an element
- remove: function( elem, types, handler, selector, mappedTypes ) {
-
- var elemData = jQuery.hasData( elem ) && jQuery._data( elem ),
- t, tns, type, origType, namespaces, origCount,
- j, events, special, handle, eventType, handleObj;
-
- if ( !elemData || !(events = elemData.events) ) {
- return;
- }
-
- // Once for each type.namespace in types; type may be omitted
- types = jQuery.trim( hoverHack( types || "" ) ).split(" ");
- for ( t = 0; t < types.length; t++ ) {
- tns = rtypenamespace.exec( types[t] ) || [];
- type = origType = tns[1];
- namespaces = tns[2];
-
- // Unbind all events (on this namespace, if provided) for the element
- if ( !type ) {
- for ( type in events ) {
- jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
- }
- continue;
- }
-
- special = jQuery.event.special[ type ] || {};
- type = ( selector? special.delegateType : special.bindType ) || type;
- eventType = events[ type ] || [];
- origCount = eventType.length;
- namespaces = namespaces ? new RegExp("(^|\\.)" + namespaces.split(".").sort().join("\\.(?:.*\\.)?") + "(\\.|$)") : null;
-
- // Remove matching events
- for ( j = 0; j < eventType.length; j++ ) {
- handleObj = eventType[ j ];
-
- if ( ( mappedTypes || origType === handleObj.origType ) &&
- ( !handler || handler.guid === handleObj.guid ) &&
- ( !namespaces || namespaces.test( handleObj.namespace ) ) &&
- ( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) {
- eventType.splice( j--, 1 );
-
- if ( handleObj.selector ) {
- eventType.delegateCount--;
- }
- if ( special.remove ) {
- special.remove.call( elem, handleObj );
- }
- }
- }
-
- // Remove generic event handler if we removed something and no more handlers exist
- // (avoids potential for endless recursion during removal of special event handlers)
- if ( eventType.length === 0 && origCount !== eventType.length ) {
- if ( !special.teardown || special.teardown.call( elem, namespaces ) === false ) {
- jQuery.removeEvent( elem, type, elemData.handle );
- }
-
- delete events[ type ];
- }
- }
-
- // Remove the expando if it's no longer used
- if ( jQuery.isEmptyObject( events ) ) {
- handle = elemData.handle;
- if ( handle ) {
- handle.elem = null;
- }
-
- // removeData also checks for emptiness and clears the expando if empty
- // so use it instead of delete
- jQuery.removeData( elem, [ "events", "handle" ], true );
- }
- },
-
- // Events that are safe to short-circuit if no handlers are attached.
- // Native DOM events should not be added, they may have inline handlers.
- customEvent: {
- "getData": true,
- "setData": true,
- "changeData": true
- },
-
- trigger: function( event, data, elem, onlyHandlers ) {
- // Don't do events on text and comment nodes
- if ( elem && (elem.nodeType === 3 || elem.nodeType === 8) ) {
- return;
- }
-
- // Event object or event type
- var type = event.type || event,
- namespaces = [],
- cache, exclusive, i, cur, old, ontype, special, handle, eventPath, bubbleType;
-
- // focus/blur morphs to focusin/out; ensure we're not firing them right now
- if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
- return;
- }
-
- if ( type.indexOf( "!" ) >= 0 ) {
- // Exclusive events trigger only for the exact event (no namespaces)
- type = type.slice(0, -1);
- exclusive = true;
- }
-
- if ( type.indexOf( "." ) >= 0 ) {
- // Namespaced trigger; create a regexp to match event type in handle()
- namespaces = type.split(".");
- type = namespaces.shift();
- namespaces.sort();
- }
-
- if ( (!elem || jQuery.event.customEvent[ type ]) && !jQuery.event.global[ type ] ) {
- // No jQuery handlers for this event type, and it can't have inline handlers
- return;
- }
-
- // Caller can pass in an Event, Object, or just an event type string
- event = typeof event === "object" ?
- // jQuery.Event object
- event[ jQuery.expando ] ? event :
- // Object literal
- new jQuery.Event( type, event ) :
- // Just the event type (string)
- new jQuery.Event( type );
-
- event.type = type;
- event.isTrigger = true;
- event.exclusive = exclusive;
- event.namespace = namespaces.join( "." );
- event.namespace_re = event.namespace? new RegExp("(^|\\.)" + namespaces.join("\\.(?:.*\\.)?") + "(\\.|$)") : null;
- ontype = type.indexOf( ":" ) < 0 ? "on" + type : "";
-
- // Handle a global trigger
- if ( !elem ) {
-
- // TODO: Stop taunting the data cache; remove global events and always attach to document
- cache = jQuery.cache;
- for ( i in cache ) {
- if ( cache[ i ].events && cache[ i ].events[ type ] ) {
- jQuery.event.trigger( event, data, cache[ i ].handle.elem, true );
- }
- }
- return;
- }
-
- // Clean up the event in case it is being reused
- event.result = undefined;
- if ( !event.target ) {
- event.target = elem;
- }
-
- // Clone any incoming data and prepend the event, creating the handler arg list
- data = data != null ? jQuery.makeArray( data ) : [];
- data.unshift( event );
-
- // Allow special events to draw outside the lines
- special = jQuery.event.special[ type ] || {};
- if ( special.trigger && special.trigger.apply( elem, data ) === false ) {
- return;
- }
-
- // Determine event propagation path in advance, per W3C events spec (#9951)
- // Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
- eventPath = [[ elem, special.bindType || type ]];
- if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
-
- bubbleType = special.delegateType || type;
- cur = rfocusMorph.test( bubbleType + type ) ? elem : elem.parentNode;
- old = null;
- for ( ; cur; cur = cur.parentNode ) {
- eventPath.push([ cur, bubbleType ]);
- old = cur;
- }
-
- // Only add window if we got to document (e.g., not plain obj or detached DOM)
- if ( old && old === elem.ownerDocument ) {
- eventPath.push([ old.defaultView || old.parentWindow || window, bubbleType ]);
- }
- }
-
- // Fire handlers on the event path
- for ( i = 0; i < eventPath.length && !event.isPropagationStopped(); i++ ) {
-
- cur = eventPath[i][0];
- event.type = eventPath[i][1];
-
- handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" );
- if ( handle ) {
- handle.apply( cur, data );
- }
- // Note that this is a bare JS function and not a jQuery handler
- handle = ontype && cur[ ontype ];
- if ( handle && jQuery.acceptData( cur ) && handle.apply( cur, data ) === false ) {
- event.preventDefault();
- }
- }
- event.type = type;
-
- // If nobody prevented the default action, do it now
- if ( !onlyHandlers && !event.isDefaultPrevented() ) {
-
- if ( (!special._default || special._default.apply( elem.ownerDocument, data ) === false) &&
- !(type === "click" && jQuery.nodeName( elem, "a" )) && jQuery.acceptData( elem ) ) {
-
- // Call a native DOM method on the target with the same name name as the event.
- // Can't use an .isFunction() check here because IE6/7 fails that test.
- // Don't do default actions on window, that's where global variables be (#6170)
- // IE<9 dies on focus/blur to hidden element (#1486)
- if ( ontype && elem[ type ] && ((type !== "focus" && type !== "blur") || event.target.offsetWidth !== 0) && !jQuery.isWindow( elem ) ) {
-
- // Don't re-trigger an onFOO event when we call its FOO() method
- old = elem[ ontype ];
-
- if ( old ) {
- elem[ ontype ] = null;
- }
-
- // Prevent re-triggering of the same event, since we already bubbled it above
- jQuery.event.triggered = type;
- elem[ type ]();
- jQuery.event.triggered = undefined;
-
- if ( old ) {
- elem[ ontype ] = old;
- }
- }
- }
- }
-
- return event.result;
- },
-
- dispatch: function( event ) {
-
- // Make a writable jQuery.Event from the native event object
- event = jQuery.event.fix( event || window.event );
-
- var handlers = ( (jQuery._data( this, "events" ) || {} )[ event.type ] || []),
- delegateCount = handlers.delegateCount,
- args = [].slice.call( arguments, 0 ),
- run_all = !event.exclusive && !event.namespace,
- special = jQuery.event.special[ event.type ] || {},
- handlerQueue = [],
- i, j, cur, jqcur, ret, selMatch, matched, matches, handleObj, sel, related;
-
- // Use the fix-ed jQuery.Event rather than the (read-only) native event
- args[0] = event;
- event.delegateTarget = this;
-
- // Call the preDispatch hook for the mapped type, and let it bail if desired
- if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
- return;
- }
-
- // Determine handlers that should run if there are delegated events
- // Avoid non-left-click bubbling in Firefox (#3861)
- if ( delegateCount && !(event.button && event.type === "click") ) {
-
- // Pregenerate a single jQuery object for reuse with .is()
- jqcur = jQuery(this);
- jqcur.context = this.ownerDocument || this;
-
- for ( cur = event.target; cur != this; cur = cur.parentNode || this ) {
-
- // Don't process events on disabled elements (#6911, #8165)
- if ( cur.disabled !== true ) {
- selMatch = {};
- matches = [];
- jqcur[0] = cur;
- for ( i = 0; i < delegateCount; i++ ) {
- handleObj = handlers[ i ];
- sel = handleObj.selector;
-
- if ( selMatch[ sel ] === undefined ) {
- selMatch[ sel ] = (
- handleObj.quick ? quickIs( cur, handleObj.quick ) : jqcur.is( sel )
- );
- }
- if ( selMatch[ sel ] ) {
- matches.push( handleObj );
- }
- }
- if ( matches.length ) {
- handlerQueue.push({ elem: cur, matches: matches });
- }
- }
- }
- }
-
- // Add the remaining (directly-bound) handlers
- if ( handlers.length > delegateCount ) {
- handlerQueue.push({ elem: this, matches: handlers.slice( delegateCount ) });
- }
-
- // Run delegates first; they may want to stop propagation beneath us
- for ( i = 0; i < handlerQueue.length && !event.isPropagationStopped(); i++ ) {
- matched = handlerQueue[ i ];
- event.currentTarget = matched.elem;
-
- for ( j = 0; j < matched.matches.length && !event.isImmediatePropagationStopped(); j++ ) {
- handleObj = matched.matches[ j ];
-
- // Triggered event must either 1) be non-exclusive and have no namespace, or
- // 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace).
- if ( run_all || (!event.namespace && !handleObj.namespace) || event.namespace_re && event.namespace_re.test( handleObj.namespace ) ) {
-
- event.data = handleObj.data;
- event.handleObj = handleObj;
-
- ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler )
- .apply( matched.elem, args );
-
- if ( ret !== undefined ) {
- event.result = ret;
- if ( ret === false ) {
- event.preventDefault();
- event.stopPropagation();
- }
- }
- }
- }
- }
-
- // Call the postDispatch hook for the mapped type
- if ( special.postDispatch ) {
- special.postDispatch.call( this, event );
- }
-
- return event.result;
- },
-
- // Includes some event props shared by KeyEvent and MouseEvent
- // *** attrChange attrName relatedNode srcElement are not normalized, non-W3C, deprecated, will be removed in 1.8 ***
- props: "attrChange attrName relatedNode srcElement altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),
-
- fixHooks: {},
-
- keyHooks: {
- props: "char charCode key keyCode".split(" "),
- filter: function( event, original ) {
-
- // Add which for key events
- if ( event.which == null ) {
- event.which = original.charCode != null ? original.charCode : original.keyCode;
- }
-
- return event;
- }
- },
-
- mouseHooks: {
- props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),
- filter: function( event, original ) {
- var eventDoc, doc, body,
- button = original.button,
- fromElement = original.fromElement;
-
- // Calculate pageX/Y if missing and clientX/Y available
- if ( event.pageX == null && original.clientX != null ) {
- eventDoc = event.target.ownerDocument || document;
- doc = eventDoc.documentElement;
- body = eventDoc.body;
-
- event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 );
- event.pageY = original.clientY + ( doc && doc.scrollTop || body && body.scrollTop || 0 ) - ( doc && doc.clientTop || body && body.clientTop || 0 );
- }
-
- // Add relatedTarget, if necessary
- if ( !event.relatedTarget && fromElement ) {
- event.relatedTarget = fromElement === event.target ? original.toElement : fromElement;
- }
-
- // Add which for click: 1 === left; 2 === middle; 3 === right
- // Note: button is not normalized, so don't use it
- if ( !event.which && button !== undefined ) {
- event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) );
- }
-
- return event;
- }
- },
-
- fix: function( event ) {
- if ( event[ jQuery.expando ] ) {
- return event;
- }
-
- // Create a writable copy of the event object and normalize some properties
- var i, prop,
- originalEvent = event,
- fixHook = jQuery.event.fixHooks[ event.type ] || {},
- copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props;
-
- event = jQuery.Event( originalEvent );
-
- for ( i = copy.length; i; ) {
- prop = copy[ --i ];
- event[ prop ] = originalEvent[ prop ];
- }
-
- // Fix target property, if necessary (#1925, IE 6/7/8 & Safari2)
- if ( !event.target ) {
- event.target = originalEvent.srcElement || document;
- }
-
- // Target should not be a text node (#504, Safari)
- if ( event.target.nodeType === 3 ) {
- event.target = event.target.parentNode;
- }
-
- // For mouse/key events; add metaKey if it's not there (#3368, IE6/7/8)
- if ( event.metaKey === undefined ) {
- event.metaKey = event.ctrlKey;
- }
-
- return fixHook.filter? fixHook.filter( event, originalEvent ) : event;
- },
-
- special: {
- ready: {
- // Make sure the ready event is setup
- setup: jQuery.bindReady
- },
-
- load: {
- // Prevent triggered image.load events from bubbling to window.load
- noBubble: true
- },
-
- focus: {
- delegateType: "focusin"
- },
- blur: {
- delegateType: "focusout"
- },
-
- beforeunload: {
- setup: function( data, namespaces, eventHandle ) {
- // We only want to do this special case on windows
- if ( jQuery.isWindow( this ) ) {
- this.onbeforeunload = eventHandle;
- }
- },
-
- teardown: function( namespaces, eventHandle ) {
- if ( this.onbeforeunload === eventHandle ) {
- this.onbeforeunload = null;
- }
- }
- }
- },
-
- simulate: function( type, elem, event, bubble ) {
- // Piggyback on a donor event to simulate a different one.
- // Fake originalEvent to avoid donor's stopPropagation, but if the
- // simulated event prevents default then we do the same on the donor.
- var e = jQuery.extend(
- new jQuery.Event(),
- event,
- { type: type,
- isSimulated: true,
- originalEvent: {}
- }
- );
- if ( bubble ) {
- jQuery.event.trigger( e, null, elem );
- } else {
- jQuery.event.dispatch.call( elem, e );
- }
- if ( e.isDefaultPrevented() ) {
- event.preventDefault();
- }
- }
-};
-
-// Some plugins are using, but it's undocumented/deprecated and will be removed.
-// The 1.7 special event interface should provide all the hooks needed now.
-jQuery.event.handle = jQuery.event.dispatch;
-
-jQuery.removeEvent = document.removeEventListener ?
- function( elem, type, handle ) {
- if ( elem.removeEventListener ) {
- elem.removeEventListener( type, handle, false );
- }
- } :
- function( elem, type, handle ) {
- if ( elem.detachEvent ) {
- elem.detachEvent( "on" + type, handle );
- }
- };
-
-jQuery.Event = function( src, props ) {
- // Allow instantiation without the 'new' keyword
- if ( !(this instanceof jQuery.Event) ) {
- return new jQuery.Event( src, props );
- }
-
- // Event object
- if ( src && src.type ) {
- this.originalEvent = src;
- this.type = src.type;
-
- // Events bubbling up the document may have been marked as prevented
- // by a handler lower down the tree; reflect the correct value.
- this.isDefaultPrevented = ( src.defaultPrevented || src.returnValue === false ||
- src.getPreventDefault && src.getPreventDefault() ) ? returnTrue : returnFalse;
-
- // Event type
- } else {
- this.type = src;
- }
-
- // Put explicitly provided properties onto the event object
- if ( props ) {
- jQuery.extend( this, props );
- }
-
- // Create a timestamp if incoming event doesn't have one
- this.timeStamp = src && src.timeStamp || jQuery.now();
-
- // Mark it as fixed
- this[ jQuery.expando ] = true;
-};
-
-function returnFalse() {
- return false;
-}
-function returnTrue() {
- return true;
-}
-
-// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
-// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
-jQuery.Event.prototype = {
- preventDefault: function() {
- this.isDefaultPrevented = returnTrue;
-
- var e = this.originalEvent;
- if ( !e ) {
- return;
- }
-
- // if preventDefault exists run it on the original event
- if ( e.preventDefault ) {
- e.preventDefault();
-
- // otherwise set the returnValue property of the original event to false (IE)
- } else {
- e.returnValue = false;
- }
- },
- stopPropagation: function() {
- this.isPropagationStopped = returnTrue;
-
- var e = this.originalEvent;
- if ( !e ) {
- return;
- }
- // if stopPropagation exists run it on the original event
- if ( e.stopPropagation ) {
- e.stopPropagation();
- }
- // otherwise set the cancelBubble property of the original event to true (IE)
- e.cancelBubble = true;
- },
- stopImmediatePropagation: function() {
- this.isImmediatePropagationStopped = returnTrue;
- this.stopPropagation();
- },
- isDefaultPrevented: returnFalse,
- isPropagationStopped: returnFalse,
- isImmediatePropagationStopped: returnFalse
-};
-
-// Create mouseenter/leave events using mouseover/out and event-time checks
-jQuery.each({
- mouseenter: "mouseover",
- mouseleave: "mouseout"
-}, function( orig, fix ) {
- jQuery.event.special[ orig ] = {
- delegateType: fix,
- bindType: fix,
-
- handle: function( event ) {
- var target = this,
- related = event.relatedTarget,
- handleObj = event.handleObj,
- selector = handleObj.selector,
- ret;
-
- // For mousenter/leave call the handler if related is outside the target.
- // NB: No relatedTarget if the mouse left/entered the browser window
- if ( !related || (related !== target && !jQuery.contains( target, related )) ) {
- event.type = handleObj.origType;
- ret = handleObj.handler.apply( this, arguments );
- event.type = fix;
- }
- return ret;
- }
- };
-});
-
-// IE submit delegation
-if ( !jQuery.support.submitBubbles ) {
-
- jQuery.event.special.submit = {
- setup: function() {
- // Only need this for delegated form submit events
- if ( jQuery.nodeName( this, "form" ) ) {
- return false;
- }
-
- // Lazy-add a submit handler when a descendant form may potentially be submitted
- jQuery.event.add( this, "click._submit keypress._submit", function( e ) {
- // Node name check avoids a VML-related crash in IE (#9807)
- var elem = e.target,
- form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined;
- if ( form && !form._submit_attached ) {
- jQuery.event.add( form, "submit._submit", function( event ) {
- event._submit_bubble = true;
- });
- form._submit_attached = true;
- }
- });
- // return undefined since we don't need an event listener
- },
-
- postDispatch: function( event ) {
- // If form was submitted by the user, bubble the event up the tree
- if ( event._submit_bubble ) {
- delete event._submit_bubble;
- if ( this.parentNode && !event.isTrigger ) {
- jQuery.event.simulate( "submit", this.parentNode, event, true );
- }
- }
- },
-
- teardown: function() {
- // Only need this for delegated form submit events
- if ( jQuery.nodeName( this, "form" ) ) {
- return false;
- }
-
- // Remove delegated handlers; cleanData eventually reaps submit handlers attached above
- jQuery.event.remove( this, "._submit" );
- }
- };
-}
-
-// IE change delegation and checkbox/radio fix
-if ( !jQuery.support.changeBubbles ) {
-
- jQuery.event.special.change = {
-
- setup: function() {
-
- if ( rformElems.test( this.nodeName ) ) {
- // IE doesn't fire change on a check/radio until blur; trigger it on click
- // after a propertychange. Eat the blur-change in special.change.handle.
- // This still fires onchange a second time for check/radio after blur.
- if ( this.type === "checkbox" || this.type === "radio" ) {
- jQuery.event.add( this, "propertychange._change", function( event ) {
- if ( event.originalEvent.propertyName === "checked" ) {
- this._just_changed = true;
- }
- });
- jQuery.event.add( this, "click._change", function( event ) {
- if ( this._just_changed && !event.isTrigger ) {
- this._just_changed = false;
- jQuery.event.simulate( "change", this, event, true );
- }
- });
- }
- return false;
- }
- // Delegated event; lazy-add a change handler on descendant inputs
- jQuery.event.add( this, "beforeactivate._change", function( e ) {
- var elem = e.target;
-
- if ( rformElems.test( elem.nodeName ) && !elem._change_attached ) {
- jQuery.event.add( elem, "change._change", function( event ) {
- if ( this.parentNode && !event.isSimulated && !event.isTrigger ) {
- jQuery.event.simulate( "change", this.parentNode, event, true );
- }
- });
- elem._change_attached = true;
- }
- });
- },
-
- handle: function( event ) {
- var elem = event.target;
-
- // Swallow native change events from checkbox/radio, we already triggered them above
- if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) {
- return event.handleObj.handler.apply( this, arguments );
- }
- },
-
- teardown: function() {
- jQuery.event.remove( this, "._change" );
-
- return rformElems.test( this.nodeName );
- }
- };
-}
-
-// Create "bubbling" focus and blur events
-if ( !jQuery.support.focusinBubbles ) {
- jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) {
-
- // Attach a single capturing handler while someone wants focusin/focusout
- var attaches = 0,
- handler = function( event ) {
- jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true );
- };
-
- jQuery.event.special[ fix ] = {
- setup: function() {
- if ( attaches++ === 0 ) {
- document.addEventListener( orig, handler, true );
- }
- },
- teardown: function() {
- if ( --attaches === 0 ) {
- document.removeEventListener( orig, handler, true );
- }
- }
- };
- });
-}
-
-jQuery.fn.extend({
-
- on: function( types, selector, data, fn, /*INTERNAL*/ one ) {
- var origFn, type;
-
- // Types can be a map of types/handlers
- if ( typeof types === "object" ) {
- // ( types-Object, selector, data )
- if ( typeof selector !== "string" ) { // && selector != null
- // ( types-Object, data )
- data = data || selector;
- selector = undefined;
- }
- for ( type in types ) {
- this.on( type, selector, data, types[ type ], one );
- }
- return this;
- }
-
- if ( data == null && fn == null ) {
- // ( types, fn )
- fn = selector;
- data = selector = undefined;
- } else if ( fn == null ) {
- if ( typeof selector === "string" ) {
- // ( types, selector, fn )
- fn = data;
- data = undefined;
- } else {
- // ( types, data, fn )
- fn = data;
- data = selector;
- selector = undefined;
- }
- }
- if ( fn === false ) {
- fn = returnFalse;
- } else if ( !fn ) {
- return this;
- }
-
- if ( one === 1 ) {
- origFn = fn;
- fn = function( event ) {
- // Can use an empty set, since event contains the info
- jQuery().off( event );
- return origFn.apply( this, arguments );
- };
- // Use same guid so caller can remove using origFn
- fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
- }
- return this.each( function() {
- jQuery.event.add( this, types, fn, data, selector );
- });
- },
- one: function( types, selector, data, fn ) {
- return this.on( types, selector, data, fn, 1 );
- },
- off: function( types, selector, fn ) {
- if ( types && types.preventDefault && types.handleObj ) {
- // ( event ) dispatched jQuery.Event
- var handleObj = types.handleObj;
- jQuery( types.delegateTarget ).off(
- handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType,
- handleObj.selector,
- handleObj.handler
- );
- return this;
- }
- if ( typeof types === "object" ) {
- // ( types-object [, selector] )
- for ( var type in types ) {
- this.off( type, selector, types[ type ] );
- }
- return this;
- }
- if ( selector === false || typeof selector === "function" ) {
- // ( types [, fn] )
- fn = selector;
- selector = undefined;
- }
- if ( fn === false ) {
- fn = returnFalse;
- }
- return this.each(function() {
- jQuery.event.remove( this, types, fn, selector );
- });
- },
-
- bind: function( types, data, fn ) {
- return this.on( types, null, data, fn );
- },
- unbind: function( types, fn ) {
- return this.off( types, null, fn );
- },
-
- live: function( types, data, fn ) {
- jQuery( this.context ).on( types, this.selector, data, fn );
- return this;
- },
- die: function( types, fn ) {
- jQuery( this.context ).off( types, this.selector || "**", fn );
- return this;
- },
-
- delegate: function( selector, types, data, fn ) {
- return this.on( types, selector, data, fn );
- },
- undelegate: function( selector, types, fn ) {
- // ( namespace ) or ( selector, types [, fn] )
- return arguments.length == 1? this.off( selector, "**" ) : this.off( types, selector, fn );
- },
-
- trigger: function( type, data ) {
- return this.each(function() {
- jQuery.event.trigger( type, data, this );
- });
- },
- triggerHandler: function( type, data ) {
- if ( this[0] ) {
- return jQuery.event.trigger( type, data, this[0], true );
- }
- },
-
- toggle: function( fn ) {
- // Save reference to arguments for access in closure
- var args = arguments,
- guid = fn.guid || jQuery.guid++,
- i = 0,
- toggler = function( event ) {
- // Figure out which function to execute
- var lastToggle = ( jQuery._data( this, "lastToggle" + fn.guid ) || 0 ) % i;
- jQuery._data( this, "lastToggle" + fn.guid, lastToggle + 1 );
-
- // Make sure that clicks stop
- event.preventDefault();
-
- // and execute the function
- return args[ lastToggle ].apply( this, arguments ) || false;
- };
-
- // link all the functions, so any of them can unbind this click handler
- toggler.guid = guid;
- while ( i < args.length ) {
- args[ i++ ].guid = guid;
- }
-
- return this.click( toggler );
- },
-
- hover: function( fnOver, fnOut ) {
- return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
- }
-});
-
-jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " +
- "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
- "change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) {
-
- // Handle event binding
- jQuery.fn[ name ] = function( data, fn ) {
- if ( fn == null ) {
- fn = data;
- data = null;
- }
-
- return arguments.length > 0 ?
- this.on( name, null, data, fn ) :
- this.trigger( name );
- };
-
- if ( jQuery.attrFn ) {
- jQuery.attrFn[ name ] = true;
- }
-
- if ( rkeyEvent.test( name ) ) {
- jQuery.event.fixHooks[ name ] = jQuery.event.keyHooks;
- }
-
- if ( rmouseEvent.test( name ) ) {
- jQuery.event.fixHooks[ name ] = jQuery.event.mouseHooks;
- }
-});
-
-
-
-/*!
- * Sizzle CSS Selector Engine
- * Copyright 2011, The Dojo Foundation
- * Released under the MIT, BSD, and GPL Licenses.
- * More information: http://sizzlejs.com/
- */
-(function(){
-
-var chunker = /((?:\((?:\([^()]+\)|[^()]+)+\)|\[(?:\[[^\[\]]*\]|['"][^'"]*['"]|[^\[\]'"]+)+\]|\\.|[^ >+~,(\[\\]+)+|[>+~])(\s*,\s*)?((?:.|\r|\n)*)/g,
- expando = "sizcache" + (Math.random() + '').replace('.', ''),
- done = 0,
- toString = Object.prototype.toString,
- hasDuplicate = false,
- baseHasDuplicate = true,
- rBackslash = /\\/g,
- rReturn = /\r\n/g,
- rNonWord = /\W/;
-
-// Here we check if the JavaScript engine is using some sort of
-// optimization where it does not always call our comparision
-// function. If that is the case, discard the hasDuplicate value.
-// Thus far that includes Google Chrome.
-[0, 0].sort(function() {
- baseHasDuplicate = false;
- return 0;
-});
-
-var Sizzle = function( selector, context, results, seed ) {
- results = results || [];
- context = context || document;
-
- var origContext = context;
-
- if ( context.nodeType !== 1 && context.nodeType !== 9 ) {
- return [];
- }
-
- if ( !selector || typeof selector !== "string" ) {
- return results;
- }
-
- var m, set, checkSet, extra, ret, cur, pop, i,
- prune = true,
- contextXML = Sizzle.isXML( context ),
- parts = [],
- soFar = selector;
-
- // Reset the position of the chunker regexp (start from head)
- do {
- chunker.exec( "" );
- m = chunker.exec( soFar );
-
- if ( m ) {
- soFar = m[3];
-
- parts.push( m[1] );
-
- if ( m[2] ) {
- extra = m[3];
- break;
- }
- }
- } while ( m );
-
- if ( parts.length > 1 && origPOS.exec( selector ) ) {
-
- if ( parts.length === 2 && Expr.relative[ parts[0] ] ) {
- set = posProcess( parts[0] + parts[1], context, seed );
-
- } else {
- set = Expr.relative[ parts[0] ] ?
- [ context ] :
- Sizzle( parts.shift(), context );
-
- while ( parts.length ) {
- selector = parts.shift();
-
- if ( Expr.relative[ selector ] ) {
- selector += parts.shift();
- }
-
- set = posProcess( selector, set, seed );
- }
- }
-
- } else {
- // Take a shortcut and set the context if the root selector is an ID
- // (but not if it'll be faster if the inner selector is an ID)
- if ( !seed && parts.length > 1 && context.nodeType === 9 && !contextXML &&
- Expr.match.ID.test(parts[0]) && !Expr.match.ID.test(parts[parts.length - 1]) ) {
-
- ret = Sizzle.find( parts.shift(), context, contextXML );
- context = ret.expr ?
- Sizzle.filter( ret.expr, ret.set )[0] :
- ret.set[0];
- }
-
- if ( context ) {
- ret = seed ?
- { expr: parts.pop(), set: makeArray(seed) } :
- Sizzle.find( parts.pop(), parts.length === 1 && (parts[0] === "~" || parts[0] === "+") && context.parentNode ? context.parentNode : context, contextXML );
-
- set = ret.expr ?
- Sizzle.filter( ret.expr, ret.set ) :
- ret.set;
-
- if ( parts.length > 0 ) {
- checkSet = makeArray( set );
-
- } else {
- prune = false;
- }
-
- while ( parts.length ) {
- cur = parts.pop();
- pop = cur;
-
- if ( !Expr.relative[ cur ] ) {
- cur = "";
- } else {
- pop = parts.pop();
- }
-
- if ( pop == null ) {
- pop = context;
- }
-
- Expr.relative[ cur ]( checkSet, pop, contextXML );
- }
-
- } else {
- checkSet = parts = [];
- }
- }
-
- if ( !checkSet ) {
- checkSet = set;
- }
-
- if ( !checkSet ) {
- Sizzle.error( cur || selector );
- }
-
- if ( toString.call(checkSet) === "[object Array]" ) {
- if ( !prune ) {
- results.push.apply( results, checkSet );
-
- } else if ( context && context.nodeType === 1 ) {
- for ( i = 0; checkSet[i] != null; i++ ) {
- if ( checkSet[i] && (checkSet[i] === true || checkSet[i].nodeType === 1 && Sizzle.contains(context, checkSet[i])) ) {
- results.push( set[i] );
- }
- }
-
- } else {
- for ( i = 0; checkSet[i] != null; i++ ) {
- if ( checkSet[i] && checkSet[i].nodeType === 1 ) {
- results.push( set[i] );
- }
- }
- }
-
- } else {
- makeArray( checkSet, results );
- }
-
- if ( extra ) {
- Sizzle( extra, origContext, results, seed );
- Sizzle.uniqueSort( results );
- }
-
- return results;
-};
-
-Sizzle.uniqueSort = function( results ) {
- if ( sortOrder ) {
- hasDuplicate = baseHasDuplicate;
- results.sort( sortOrder );
-
- if ( hasDuplicate ) {
- for ( var i = 1; i < results.length; i++ ) {
- if ( results[i] === results[ i - 1 ] ) {
- results.splice( i--, 1 );
- }
- }
- }
- }
-
- return results;
-};
-
-Sizzle.matches = function( expr, set ) {
- return Sizzle( expr, null, null, set );
-};
-
-Sizzle.matchesSelector = function( node, expr ) {
- return Sizzle( expr, null, null, [node] ).length > 0;
-};
-
-Sizzle.find = function( expr, context, isXML ) {
- var set, i, len, match, type, left;
-
- if ( !expr ) {
- return [];
- }
-
- for ( i = 0, len = Expr.order.length; i < len; i++ ) {
- type = Expr.order[i];
-
- if ( (match = Expr.leftMatch[ type ].exec( expr )) ) {
- left = match[1];
- match.splice( 1, 1 );
-
- if ( left.substr( left.length - 1 ) !== "\\" ) {
- match[1] = (match[1] || "").replace( rBackslash, "" );
- set = Expr.find[ type ]( match, context, isXML );
-
- if ( set != null ) {
- expr = expr.replace( Expr.match[ type ], "" );
- break;
- }
- }
- }
- }
-
- if ( !set ) {
- set = typeof context.getElementsByTagName !== "undefined" ?
- context.getElementsByTagName( "*" ) :
- [];
- }
-
- return { set: set, expr: expr };
-};
-
-Sizzle.filter = function( expr, set, inplace, not ) {
- var match, anyFound,
- type, found, item, filter, left,
- i, pass,
- old = expr,
- result = [],
- curLoop = set,
- isXMLFilter = set && set[0] && Sizzle.isXML( set[0] );
-
- while ( expr && set.length ) {
- for ( type in Expr.filter ) {
- if ( (match = Expr.leftMatch[ type ].exec( expr )) != null && match[2] ) {
- filter = Expr.filter[ type ];
- left = match[1];
-
- anyFound = false;
-
- match.splice(1,1);
-
- if ( left.substr( left.length - 1 ) === "\\" ) {
- continue;
- }
-
- if ( curLoop === result ) {
- result = [];
- }
-
- if ( Expr.preFilter[ type ] ) {
- match = Expr.preFilter[ type ]( match, curLoop, inplace, result, not, isXMLFilter );
-
- if ( !match ) {
- anyFound = found = true;
-
- } else if ( match === true ) {
- continue;
- }
- }
-
- if ( match ) {
- for ( i = 0; (item = curLoop[i]) != null; i++ ) {
- if ( item ) {
- found = filter( item, match, i, curLoop );
- pass = not ^ found;
-
- if ( inplace && found != null ) {
- if ( pass ) {
- anyFound = true;
-
- } else {
- curLoop[i] = false;
- }
-
- } else if ( pass ) {
- result.push( item );
- anyFound = true;
- }
- }
- }
- }
-
- if ( found !== undefined ) {
- if ( !inplace ) {
- curLoop = result;
- }
-
- expr = expr.replace( Expr.match[ type ], "" );
-
- if ( !anyFound ) {
- return [];
- }
-
- break;
- }
- }
- }
-
- // Improper expression
- if ( expr === old ) {
- if ( anyFound == null ) {
- Sizzle.error( expr );
-
- } else {
- break;
- }
- }
-
- old = expr;
- }
-
- return curLoop;
-};
-
-Sizzle.error = function( msg ) {
- throw new Error( "Syntax error, unrecognized expression: " + msg );
-};
-
-/**
- * Utility function for retreiving the text value of an array of DOM nodes
- * @param {Array|Element} elem
- */
-var getText = Sizzle.getText = function( elem ) {
- var i, node,
- nodeType = elem.nodeType,
- ret = "";
-
- if ( nodeType ) {
- if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
- // Use textContent || innerText for elements
- if ( typeof elem.textContent === 'string' ) {
- return elem.textContent;
- } else if ( typeof elem.innerText === 'string' ) {
- // Replace IE's carriage returns
- return elem.innerText.replace( rReturn, '' );
- } else {
- // Traverse it's children
- for ( elem = elem.firstChild; elem; elem = elem.nextSibling) {
- ret += getText( elem );
- }
- }
- } else if ( nodeType === 3 || nodeType === 4 ) {
- return elem.nodeValue;
- }
- } else {
-
- // If no nodeType, this is expected to be an array
- for ( i = 0; (node = elem[i]); i++ ) {
- // Do not traverse comment nodes
- if ( node.nodeType !== 8 ) {
- ret += getText( node );
- }
- }
- }
- return ret;
-};
-
-var Expr = Sizzle.selectors = {
- order: [ "ID", "NAME", "TAG" ],
-
- match: {
- ID: /#((?:[\w\u00c0-\uFFFF\-]|\\.)+)/,
- CLASS: /\.((?:[\w\u00c0-\uFFFF\-]|\\.)+)/,
- NAME: /\[name=['"]*((?:[\w\u00c0-\uFFFF\-]|\\.)+)['"]*\]/,
- ATTR: /\[\s*((?:[\w\u00c0-\uFFFF\-]|\\.)+)\s*(?:(\S?=)\s*(?:(['"])(.*?)\3|(#?(?:[\w\u00c0-\uFFFF\-]|\\.)*)|)|)\s*\]/,
- TAG: /^((?:[\w\u00c0-\uFFFF\*\-]|\\.)+)/,
- CHILD: /:(only|nth|last|first)-child(?:\(\s*(even|odd|(?:[+\-]?\d+|(?:[+\-]?\d*)?n\s*(?:[+\-]\s*\d+)?))\s*\))?/,
- POS: /:(nth|eq|gt|lt|first|last|even|odd)(?:\((\d*)\))?(?=[^\-]|$)/,
- PSEUDO: /:((?:[\w\u00c0-\uFFFF\-]|\\.)+)(?:\((['"]?)((?:\([^\)]+\)|[^\(\)]*)+)\2\))?/
- },
-
- leftMatch: {},
-
- attrMap: {
- "class": "className",
- "for": "htmlFor"
- },
-
- attrHandle: {
- href: function( elem ) {
- return elem.getAttribute( "href" );
- },
- type: function( elem ) {
- return elem.getAttribute( "type" );
- }
- },
-
- relative: {
- "+": function(checkSet, part){
- var isPartStr = typeof part === "string",
- isTag = isPartStr && !rNonWord.test( part ),
- isPartStrNotTag = isPartStr && !isTag;
-
- if ( isTag ) {
- part = part.toLowerCase();
- }
-
- for ( var i = 0, l = checkSet.length, elem; i < l; i++ ) {
- if ( (elem = checkSet[i]) ) {
- while ( (elem = elem.previousSibling) && elem.nodeType !== 1 ) {}
-
- checkSet[i] = isPartStrNotTag || elem && elem.nodeName.toLowerCase() === part ?
- elem || false :
- elem === part;
- }
- }
-
- if ( isPartStrNotTag ) {
- Sizzle.filter( part, checkSet, true );
- }
- },
-
- ">": function( checkSet, part ) {
- var elem,
- isPartStr = typeof part === "string",
- i = 0,
- l = checkSet.length;
-
- if ( isPartStr && !rNonWord.test( part ) ) {
- part = part.toLowerCase();
-
- for ( ; i < l; i++ ) {
- elem = checkSet[i];
-
- if ( elem ) {
- var parent = elem.parentNode;
- checkSet[i] = parent.nodeName.toLowerCase() === part ? parent : false;
- }
- }
-
- } else {
- for ( ; i < l; i++ ) {
- elem = checkSet[i];
-
- if ( elem ) {
- checkSet[i] = isPartStr ?
- elem.parentNode :
- elem.parentNode === part;
- }
- }
-
- if ( isPartStr ) {
- Sizzle.filter( part, checkSet, true );
- }
- }
- },
-
- "": function(checkSet, part, isXML){
- var nodeCheck,
- doneName = done++,
- checkFn = dirCheck;
-
- if ( typeof part === "string" && !rNonWord.test( part ) ) {
- part = part.toLowerCase();
- nodeCheck = part;
- checkFn = dirNodeCheck;
- }
-
- checkFn( "parentNode", part, doneName, checkSet, nodeCheck, isXML );
- },
-
- "~": function( checkSet, part, isXML ) {
- var nodeCheck,
- doneName = done++,
- checkFn = dirCheck;
-
- if ( typeof part === "string" && !rNonWord.test( part ) ) {
- part = part.toLowerCase();
- nodeCheck = part;
- checkFn = dirNodeCheck;
- }
-
- checkFn( "previousSibling", part, doneName, checkSet, nodeCheck, isXML );
- }
- },
-
- find: {
- ID: function( match, context, isXML ) {
- if ( typeof context.getElementById !== "undefined" && !isXML ) {
- var m = context.getElementById(match[1]);
- // Check parentNode to catch when Blackberry 4.6 returns
- // nodes that are no longer in the document #6963
- return m && m.parentNode ? [m] : [];
- }
- },
-
- NAME: function( match, context ) {
- if ( typeof context.getElementsByName !== "undefined" ) {
- var ret = [],
- results = context.getElementsByName( match[1] );
-
- for ( var i = 0, l = results.length; i < l; i++ ) {
- if ( results[i].getAttribute("name") === match[1] ) {
- ret.push( results[i] );
- }
- }
-
- return ret.length === 0 ? null : ret;
- }
- },
-
- TAG: function( match, context ) {
- if ( typeof context.getElementsByTagName !== "undefined" ) {
- return context.getElementsByTagName( match[1] );
- }
- }
- },
- preFilter: {
- CLASS: function( match, curLoop, inplace, result, not, isXML ) {
- match = " " + match[1].replace( rBackslash, "" ) + " ";
-
- if ( isXML ) {
- return match;
- }
-
- for ( var i = 0, elem; (elem = curLoop[i]) != null; i++ ) {
- if ( elem ) {
- if ( not ^ (elem.className && (" " + elem.className + " ").replace(/[\t\n\r]/g, " ").indexOf(match) >= 0) ) {
- if ( !inplace ) {
- result.push( elem );
- }
-
- } else if ( inplace ) {
- curLoop[i] = false;
- }
- }
- }
-
- return false;
- },
-
- ID: function( match ) {
- return match[1].replace( rBackslash, "" );
- },
-
- TAG: function( match, curLoop ) {
- return match[1].replace( rBackslash, "" ).toLowerCase();
- },
-
- CHILD: function( match ) {
- if ( match[1] === "nth" ) {
- if ( !match[2] ) {
- Sizzle.error( match[0] );
- }
-
- match[2] = match[2].replace(/^\+|\s*/g, '');
-
- // parse equations like 'even', 'odd', '5', '2n', '3n+2', '4n-1', '-n+6'
- var test = /(-?)(\d*)(?:n([+\-]?\d*))?/.exec(
- match[2] === "even" && "2n" || match[2] === "odd" && "2n+1" ||
- !/\D/.test( match[2] ) && "0n+" + match[2] || match[2]);
-
- // calculate the numbers (first)n+(last) including if they are negative
- match[2] = (test[1] + (test[2] || 1)) - 0;
- match[3] = test[3] - 0;
- }
- else if ( match[2] ) {
- Sizzle.error( match[0] );
- }
-
- // TODO: Move to normal caching system
- match[0] = done++;
-
- return match;
- },
-
- ATTR: function( match, curLoop, inplace, result, not, isXML ) {
- var name = match[1] = match[1].replace( rBackslash, "" );
-
- if ( !isXML && Expr.attrMap[name] ) {
- match[1] = Expr.attrMap[name];
- }
-
- // Handle if an un-quoted value was used
- match[4] = ( match[4] || match[5] || "" ).replace( rBackslash, "" );
-
- if ( match[2] === "~=" ) {
- match[4] = " " + match[4] + " ";
- }
-
- return match;
- },
-
- PSEUDO: function( match, curLoop, inplace, result, not ) {
- if ( match[1] === "not" ) {
- // If we're dealing with a complex expression, or a simple one
- if ( ( chunker.exec(match[3]) || "" ).length > 1 || /^\w/.test(match[3]) ) {
- match[3] = Sizzle(match[3], null, null, curLoop);
-
- } else {
- var ret = Sizzle.filter(match[3], curLoop, inplace, true ^ not);
-
- if ( !inplace ) {
- result.push.apply( result, ret );
- }
-
- return false;
- }
-
- } else if ( Expr.match.POS.test( match[0] ) || Expr.match.CHILD.test( match[0] ) ) {
- return true;
- }
-
- return match;
- },
-
- POS: function( match ) {
- match.unshift( true );
-
- return match;
- }
- },
-
- filters: {
- enabled: function( elem ) {
- return elem.disabled === false && elem.type !== "hidden";
- },
-
- disabled: function( elem ) {
- return elem.disabled === true;
- },
-
- checked: function( elem ) {
- return elem.checked === true;
- },
-
- selected: function( elem ) {
- // Accessing this property makes selected-by-default
- // options in Safari work properly
- if ( elem.parentNode ) {
- elem.parentNode.selectedIndex;
- }
-
- return elem.selected === true;
- },
-
- parent: function( elem ) {
- return !!elem.firstChild;
- },
-
- empty: function( elem ) {
- return !elem.firstChild;
- },
-
- has: function( elem, i, match ) {
- return !!Sizzle( match[3], elem ).length;
- },
-
- header: function( elem ) {
- return (/h\d/i).test( elem.nodeName );
- },
-
- text: function( elem ) {
- var attr = elem.getAttribute( "type" ), type = elem.type;
- // IE6 and 7 will map elem.type to 'text' for new HTML5 types (search, etc)
- // use getAttribute instead to test this case
- return elem.nodeName.toLowerCase() === "input" && "text" === type && ( attr === type || attr === null );
- },
-
- radio: function( elem ) {
- return elem.nodeName.toLowerCase() === "input" && "radio" === elem.type;
- },
-
- checkbox: function( elem ) {
- return elem.nodeName.toLowerCase() === "input" && "checkbox" === elem.type;
- },
-
- file: function( elem ) {
- return elem.nodeName.toLowerCase() === "input" && "file" === elem.type;
- },
-
- password: function( elem ) {
- return elem.nodeName.toLowerCase() === "input" && "password" === elem.type;
- },
-
- submit: function( elem ) {
- var name = elem.nodeName.toLowerCase();
- return (name === "input" || name === "button") && "submit" === elem.type;
- },
-
- image: function( elem ) {
- return elem.nodeName.toLowerCase() === "input" && "image" === elem.type;
- },
-
- reset: function( elem ) {
- var name = elem.nodeName.toLowerCase();
- return (name === "input" || name === "button") && "reset" === elem.type;
- },
-
- button: function( elem ) {
- var name = elem.nodeName.toLowerCase();
- return name === "input" && "button" === elem.type || name === "button";
- },
-
- input: function( elem ) {
- return (/input|select|textarea|button/i).test( elem.nodeName );
- },
-
- focus: function( elem ) {
- return elem === elem.ownerDocument.activeElement;
- }
- },
- setFilters: {
- first: function( elem, i ) {
- return i === 0;
- },
-
- last: function( elem, i, match, array ) {
- return i === array.length - 1;
- },
-
- even: function( elem, i ) {
- return i % 2 === 0;
- },
-
- odd: function( elem, i ) {
- return i % 2 === 1;
- },
-
- lt: function( elem, i, match ) {
- return i < match[3] - 0;
- },
-
- gt: function( elem, i, match ) {
- return i > match[3] - 0;
- },
-
- nth: function( elem, i, match ) {
- return match[3] - 0 === i;
- },
-
- eq: function( elem, i, match ) {
- return match[3] - 0 === i;
- }
- },
- filter: {
- PSEUDO: function( elem, match, i, array ) {
- var name = match[1],
- filter = Expr.filters[ name ];
-
- if ( filter ) {
- return filter( elem, i, match, array );
-
- } else if ( name === "contains" ) {
- return (elem.textContent || elem.innerText || getText([ elem ]) || "").indexOf(match[3]) >= 0;
-
- } else if ( name === "not" ) {
- var not = match[3];
-
- for ( var j = 0, l = not.length; j < l; j++ ) {
- if ( not[j] === elem ) {
- return false;
- }
- }
-
- return true;
-
- } else {
- Sizzle.error( name );
- }
- },
-
- CHILD: function( elem, match ) {
- var first, last,
- doneName, parent, cache,
- count, diff,
- type = match[1],
- node = elem;
-
- switch ( type ) {
- case "only":
- case "first":
- while ( (node = node.previousSibling) ) {
- if ( node.nodeType === 1 ) {
- return false;
- }
- }
-
- if ( type === "first" ) {
- return true;
- }
-
- node = elem;
-
- /* falls through */
- case "last":
- while ( (node = node.nextSibling) ) {
- if ( node.nodeType === 1 ) {
- return false;
- }
- }
-
- return true;
-
- case "nth":
- first = match[2];
- last = match[3];
-
- if ( first === 1 && last === 0 ) {
- return true;
- }
-
- doneName = match[0];
- parent = elem.parentNode;
-
- if ( parent && (parent[ expando ] !== doneName || !elem.nodeIndex) ) {
- count = 0;
-
- for ( node = parent.firstChild; node; node = node.nextSibling ) {
- if ( node.nodeType === 1 ) {
- node.nodeIndex = ++count;
- }
- }
-
- parent[ expando ] = doneName;
- }
-
- diff = elem.nodeIndex - last;
-
- if ( first === 0 ) {
- return diff === 0;
-
- } else {
- return ( diff % first === 0 && diff / first >= 0 );
- }
- }
- },
-
- ID: function( elem, match ) {
- return elem.nodeType === 1 && elem.getAttribute("id") === match;
- },
-
- TAG: function( elem, match ) {
- return (match === "*" && elem.nodeType === 1) || !!elem.nodeName && elem.nodeName.toLowerCase() === match;
- },
-
- CLASS: function( elem, match ) {
- return (" " + (elem.className || elem.getAttribute("class")) + " ")
- .indexOf( match ) > -1;
- },
-
- ATTR: function( elem, match ) {
- var name = match[1],
- result = Sizzle.attr ?
- Sizzle.attr( elem, name ) :
- Expr.attrHandle[ name ] ?
- Expr.attrHandle[ name ]( elem ) :
- elem[ name ] != null ?
- elem[ name ] :
- elem.getAttribute( name ),
- value = result + "",
- type = match[2],
- check = match[4];
-
- return result == null ?
- type === "!=" :
- !type && Sizzle.attr ?
- result != null :
- type === "=" ?
- value === check :
- type === "*=" ?
- value.indexOf(check) >= 0 :
- type === "~=" ?
- (" " + value + " ").indexOf(check) >= 0 :
- !check ?
- value && result !== false :
- type === "!=" ?
- value !== check :
- type === "^=" ?
- value.indexOf(check) === 0 :
- type === "$=" ?
- value.substr(value.length - check.length) === check :
- type === "|=" ?
- value === check || value.substr(0, check.length + 1) === check + "-" :
- false;
- },
-
- POS: function( elem, match, i, array ) {
- var name = match[2],
- filter = Expr.setFilters[ name ];
-
- if ( filter ) {
- return filter( elem, i, match, array );
- }
- }
- }
-};
-
-var origPOS = Expr.match.POS,
- fescape = function(all, num){
- return "\\" + (num - 0 + 1);
- };
-
-for ( var type in Expr.match ) {
- Expr.match[ type ] = new RegExp( Expr.match[ type ].source + (/(?![^\[]*\])(?![^\(]*\))/.source) );
- Expr.leftMatch[ type ] = new RegExp( /(^(?:.|\r|\n)*?)/.source + Expr.match[ type ].source.replace(/\\(\d+)/g, fescape) );
-}
-// Expose origPOS
-// "global" as in regardless of relation to brackets/parens
-Expr.match.globalPOS = origPOS;
-
-var makeArray = function( array, results ) {
- array = Array.prototype.slice.call( array, 0 );
-
- if ( results ) {
- results.push.apply( results, array );
- return results;
- }
-
- return array;
-};
-
-// Perform a simple check to determine if the browser is capable of
-// converting a NodeList to an array using builtin methods.
-// Also verifies that the returned array holds DOM nodes
-// (which is not the case in the Blackberry browser)
-try {
- Array.prototype.slice.call( document.documentElement.childNodes, 0 )[0].nodeType;
-
-// Provide a fallback method if it does not work
-} catch( e ) {
- makeArray = function( array, results ) {
- var i = 0,
- ret = results || [];
-
- if ( toString.call(array) === "[object Array]" ) {
- Array.prototype.push.apply( ret, array );
-
- } else {
- if ( typeof array.length === "number" ) {
- for ( var l = array.length; i < l; i++ ) {
- ret.push( array[i] );
- }
-
- } else {
- for ( ; array[i]; i++ ) {
- ret.push( array[i] );
- }
- }
- }
-
- return ret;
- };
-}
-
-var sortOrder, siblingCheck;
-
-if ( document.documentElement.compareDocumentPosition ) {
- sortOrder = function( a, b ) {
- if ( a === b ) {
- hasDuplicate = true;
- return 0;
- }
-
- if ( !a.compareDocumentPosition || !b.compareDocumentPosition ) {
- return a.compareDocumentPosition ? -1 : 1;
- }
-
- return a.compareDocumentPosition(b) & 4 ? -1 : 1;
- };
-
-} else {
- sortOrder = function( a, b ) {
- // The nodes are identical, we can exit early
- if ( a === b ) {
- hasDuplicate = true;
- return 0;
-
- // Fallback to using sourceIndex (in IE) if it's available on both nodes
- } else if ( a.sourceIndex && b.sourceIndex ) {
- return a.sourceIndex - b.sourceIndex;
- }
-
- var al, bl,
- ap = [],
- bp = [],
- aup = a.parentNode,
- bup = b.parentNode,
- cur = aup;
-
- // If the nodes are siblings (or identical) we can do a quick check
- if ( aup === bup ) {
- return siblingCheck( a, b );
-
- // If no parents were found then the nodes are disconnected
- } else if ( !aup ) {
- return -1;
-
- } else if ( !bup ) {
- return 1;
- }
-
- // Otherwise they're somewhere else in the tree so we need
- // to build up a full list of the parentNodes for comparison
- while ( cur ) {
- ap.unshift( cur );
- cur = cur.parentNode;
- }
-
- cur = bup;
-
- while ( cur ) {
- bp.unshift( cur );
- cur = cur.parentNode;
- }
-
- al = ap.length;
- bl = bp.length;
-
- // Start walking down the tree looking for a discrepancy
- for ( var i = 0; i < al && i < bl; i++ ) {
- if ( ap[i] !== bp[i] ) {
- return siblingCheck( ap[i], bp[i] );
- }
- }
-
- // We ended someplace up the tree so do a sibling check
- return i === al ?
- siblingCheck( a, bp[i], -1 ) :
- siblingCheck( ap[i], b, 1 );
- };
-
- siblingCheck = function( a, b, ret ) {
- if ( a === b ) {
- return ret;
- }
-
- var cur = a.nextSibling;
-
- while ( cur ) {
- if ( cur === b ) {
- return -1;
- }
-
- cur = cur.nextSibling;
- }
-
- return 1;
- };
-}
-
-// Check to see if the browser returns elements by name when
-// querying by getElementById (and provide a workaround)
-(function(){
- // We're going to inject a fake input element with a specified name
- var form = document.createElement("div"),
- id = "script" + (new Date()).getTime(),
- root = document.documentElement;
-
- form.innerHTML = "<a name='" + id + "'/>";
-
- // Inject it into the root element, check its status, and remove it quickly
- root.insertBefore( form, root.firstChild );
-
- // The workaround has to do additional checks after a getElementById
- // Which slows things down for other browsers (hence the branching)
- if ( document.getElementById( id ) ) {
- Expr.find.ID = function( match, context, isXML ) {
- if ( typeof context.getElementById !== "undefined" && !isXML ) {
- var m = context.getElementById(match[1]);
-
- return m ?
- m.id === match[1] || typeof m.getAttributeNode !== "undefined" && m.getAttributeNode("id").nodeValue === match[1] ?
- [m] :
- undefined :
- [];
- }
- };
-
- Expr.filter.ID = function( elem, match ) {
- var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id");
-
- return elem.nodeType === 1 && node && node.nodeValue === match;
- };
- }
-
- root.removeChild( form );
-
- // release memory in IE
- root = form = null;
-})();
-
-(function(){
- // Check to see if the browser returns only elements
- // when doing getElementsByTagName("*")
-
- // Create a fake element
- var div = document.createElement("div");
- div.appendChild( document.createComment("") );
-
- // Make sure no comments are found
- if ( div.getElementsByTagName("*").length > 0 ) {
- Expr.find.TAG = function( match, context ) {
- var results = context.getElementsByTagName( match[1] );
-
- // Filter out possible comments
- if ( match[1] === "*" ) {
- var tmp = [];
-
- for ( var i = 0; results[i]; i++ ) {
- if ( results[i].nodeType === 1 ) {
- tmp.push( results[i] );
- }
- }
-
- results = tmp;
- }
-
- return results;
- };
- }
-
- // Check to see if an attribute returns normalized href attributes
- div.innerHTML = "<a href='#'></a>";
-
- if ( div.firstChild && typeof div.firstChild.getAttribute !== "undefined" &&
- div.firstChild.getAttribute("href") !== "#" ) {
-
- Expr.attrHandle.href = function( elem ) {
- return elem.getAttribute( "href", 2 );
- };
- }
-
- // release memory in IE
- div = null;
-})();
-
-if ( document.querySelectorAll ) {
- (function(){
- var oldSizzle = Sizzle,
- div = document.createElement("div"),
- id = "__sizzle__";
-
- div.innerHTML = "<p class='TEST'></p>";
-
- // Safari can't handle uppercase or unicode characters when
- // in quirks mode.
- if ( div.querySelectorAll && div.querySelectorAll(".TEST").length === 0 ) {
- return;
- }
-
- Sizzle = function( query, context, extra, seed ) {
- context = context || document;
-
- // Only use querySelectorAll on non-XML documents
- // (ID selectors don't work in non-HTML documents)
- if ( !seed && !Sizzle.isXML(context) ) {
- // See if we find a selector to speed up
- var match = /^(\w+$)|^\.([\w\-]+$)|^#([\w\-]+$)/.exec( query );
-
- if ( match && (context.nodeType === 1 || context.nodeType === 9) ) {
- // Speed-up: Sizzle("TAG")
- if ( match[1] ) {
- return makeArray( context.getElementsByTagName( query ), extra );
-
- // Speed-up: Sizzle(".CLASS")
- } else if ( match[2] && Expr.find.CLASS && context.getElementsByClassName ) {
- return makeArray( context.getElementsByClassName( match[2] ), extra );
- }
- }
-
- if ( context.nodeType === 9 ) {
- // Speed-up: Sizzle("body")
- // The body element only exists once, optimize finding it
- if ( query === "body" && context.body ) {
- return makeArray( [ context.body ], extra );
-
- // Speed-up: Sizzle("#ID")
- } else if ( match && match[3] ) {
- var elem = context.getElementById( match[3] );
-
- // Check parentNode to catch when Blackberry 4.6 returns
- // nodes that are no longer in the document #6963
- if ( elem && elem.parentNode ) {
- // Handle the case where IE and Opera return items
- // by name instead of ID
- if ( elem.id === match[3] ) {
- return makeArray( [ elem ], extra );
- }
-
- } else {
- return makeArray( [], extra );
- }
- }
-
- try {
- return makeArray( context.querySelectorAll(query), extra );
- } catch(qsaError) {}
-
- // qSA works strangely on Element-rooted queries
- // We can work around this by specifying an extra ID on the root
- // and working up from there (Thanks to Andrew Dupont for the technique)
- // IE 8 doesn't work on object elements
- } else if ( context.nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) {
- var oldContext = context,
- old = context.getAttribute( "id" ),
- nid = old || id,
- hasParent = context.parentNode,
- relativeHierarchySelector = /^\s*[+~]/.test( query );
-
- if ( !old ) {
- context.setAttribute( "id", nid );
- } else {
- nid = nid.replace( /'/g, "\\$&" );
- }
- if ( relativeHierarchySelector && hasParent ) {
- context = context.parentNode;
- }
-
- try {
- if ( !relativeHierarchySelector || hasParent ) {
- return makeArray( context.querySelectorAll( "[id='" + nid + "'] " + query ), extra );
- }
-
- } catch(pseudoError) {
- } finally {
- if ( !old ) {
- oldContext.removeAttribute( "id" );
- }
- }
- }
- }
-
- return oldSizzle(query, context, extra, seed);
- };
-
- for ( var prop in oldSizzle ) {
- Sizzle[ prop ] = oldSizzle[ prop ];
- }
-
- // release memory in IE
- div = null;
- })();
-}
-
-(function(){
- var html = document.documentElement,
- matches = html.matchesSelector || html.mozMatchesSelector || html.webkitMatchesSelector || html.msMatchesSelector;
-
- if ( matches ) {
- // Check to see if it's possible to do matchesSelector
- // on a disconnected node (IE 9 fails this)
- var disconnectedMatch = !matches.call( document.createElement( "div" ), "div" ),
- pseudoWorks = false;
-
- try {
- // This should fail with an exception
- // Gecko does not error, returns false instead
- matches.call( document.documentElement, "[test!='']:sizzle" );
-
- } catch( pseudoError ) {
- pseudoWorks = true;
- }
-
- Sizzle.matchesSelector = function( node, expr ) {
- // Make sure that attribute selectors are quoted
- expr = expr.replace(/\=\s*([^'"\]]*)\s*\]/g, "='$1']");
-
- if ( !Sizzle.isXML( node ) ) {
- try {
- if ( pseudoWorks || !Expr.match.PSEUDO.test( expr ) && !/!=/.test( expr ) ) {
- var ret = matches.call( node, expr );
-
- // IE 9's matchesSelector returns false on disconnected nodes
- if ( ret || !disconnectedMatch ||
- // As well, disconnected nodes are said to be in a document
- // fragment in IE 9, so check for that
- node.document && node.document.nodeType !== 11 ) {
- return ret;
- }
- }
- } catch(e) {}
- }
-
- return Sizzle(expr, null, null, [node]).length > 0;
- };
- }
-})();
-
-(function(){
- var div = document.createElement("div");
-
- div.innerHTML = "<div class='test e'></div><div class='test'></div>";
-
- // Opera can't find a second classname (in 9.6)
- // Also, make sure that getElementsByClassName actually exists
- if ( !div.getElementsByClassName || div.getElementsByClassName("e").length === 0 ) {
- return;
- }
-
- // Safari caches class attributes, doesn't catch changes (in 3.2)
- div.lastChild.className = "e";
-
- if ( div.getElementsByClassName("e").length === 1 ) {
- return;
- }
-
- Expr.order.splice(1, 0, "CLASS");
- Expr.find.CLASS = function( match, context, isXML ) {
- if ( typeof context.getElementsByClassName !== "undefined" && !isXML ) {
- return context.getElementsByClassName(match[1]);
- }
- };
-
- // release memory in IE
- div = null;
-})();
-
-function dirNodeCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) {
- for ( var i = 0, l = checkSet.length; i < l; i++ ) {
- var elem = checkSet[i];
-
- if ( elem ) {
- var match = false;
-
- elem = elem[dir];
-
- while ( elem ) {
- if ( elem[ expando ] === doneName ) {
- match = checkSet[elem.sizset];
- break;
- }
-
- if ( elem.nodeType === 1 && !isXML ){
- elem[ expando ] = doneName;
- elem.sizset = i;
- }
-
- if ( elem.nodeName.toLowerCase() === cur ) {
- match = elem;
- break;
- }
-
- elem = elem[dir];
- }
-
- checkSet[i] = match;
- }
- }
-}
-
-function dirCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) {
- for ( var i = 0, l = checkSet.length; i < l; i++ ) {
- var elem = checkSet[i];
-
- if ( elem ) {
- var match = false;
-
- elem = elem[dir];
-
- while ( elem ) {
- if ( elem[ expando ] === doneName ) {
- match = checkSet[elem.sizset];
- break;
- }
-
- if ( elem.nodeType === 1 ) {
- if ( !isXML ) {
- elem[ expando ] = doneName;
- elem.sizset = i;
- }
-
- if ( typeof cur !== "string" ) {
- if ( elem === cur ) {
- match = true;
- break;
- }
-
- } else if ( Sizzle.filter( cur, [elem] ).length > 0 ) {
- match = elem;
- break;
- }
- }
-
- elem = elem[dir];
- }
-
- checkSet[i] = match;
- }
- }
-}
-
-if ( document.documentElement.contains ) {
- Sizzle.contains = function( a, b ) {
- return a !== b && (a.contains ? a.contains(b) : true);
- };
-
-} else if ( document.documentElement.compareDocumentPosition ) {
- Sizzle.contains = function( a, b ) {
- return !!(a.compareDocumentPosition(b) & 16);
- };
-
-} else {
- Sizzle.contains = function() {
- return false;
- };
-}
-
-Sizzle.isXML = function( elem ) {
- // documentElement is verified for cases where it doesn't yet exist
- // (such as loading iframes in IE - #4833)
- var documentElement = (elem ? elem.ownerDocument || elem : 0).documentElement;
-
- return documentElement ? documentElement.nodeName !== "HTML" : false;
-};
-
-var posProcess = function( selector, context, seed ) {
- var match,
- tmpSet = [],
- later = "",
- root = context.nodeType ? [context] : context;
-
- // Position selectors must be done after the filter
- // And so must :not(positional) so we move all PSEUDOs to the end
- while ( (match = Expr.match.PSEUDO.exec( selector )) ) {
- later += match[0];
- selector = selector.replace( Expr.match.PSEUDO, "" );
- }
-
- selector = Expr.relative[selector] ? selector + "*" : selector;
-
- for ( var i = 0, l = root.length; i < l; i++ ) {
- Sizzle( selector, root[i], tmpSet, seed );
- }
-
- return Sizzle.filter( later, tmpSet );
-};
-
-// EXPOSE
-// Override sizzle attribute retrieval
-Sizzle.attr = jQuery.attr;
-Sizzle.selectors.attrMap = {};
-jQuery.find = Sizzle;
-jQuery.expr = Sizzle.selectors;
-jQuery.expr[":"] = jQuery.expr.filters;
-jQuery.unique = Sizzle.uniqueSort;
-jQuery.text = Sizzle.getText;
-jQuery.isXMLDoc = Sizzle.isXML;
-jQuery.contains = Sizzle.contains;
-
-
-})();
-
-
-var runtil = /Until$/,
- rparentsprev = /^(?:parents|prevUntil|prevAll)/,
- // Note: This RegExp should be improved, or likely pulled from Sizzle
- rmultiselector = /,/,
- isSimple = /^.[^:#\[\.,]*$/,
- slice = Array.prototype.slice,
- POS = jQuery.expr.match.globalPOS,
- // methods guaranteed to produce a unique set when starting from a unique set
- guaranteedUnique = {
- children: true,
- contents: true,
- next: true,
- prev: true
- };
-
-jQuery.fn.extend({
- find: function( selector ) {
- var self = this,
- i, l;
-
- if ( typeof selector !== "string" ) {
- return jQuery( selector ).filter(function() {
- for ( i = 0, l = self.length; i < l; i++ ) {
- if ( jQuery.contains( self[ i ], this ) ) {
- return true;
- }
- }
- });
- }
-
- var ret = this.pushStack( "", "find", selector ),
- length, n, r;
-
- for ( i = 0, l = this.length; i < l; i++ ) {
- length = ret.length;
- jQuery.find( selector, this[i], ret );
-
- if ( i > 0 ) {
- // Make sure that the results are unique
- for ( n = length; n < ret.length; n++ ) {
- for ( r = 0; r < length; r++ ) {
- if ( ret[r] === ret[n] ) {
- ret.splice(n--, 1);
- break;
- }
- }
- }
- }
- }
-
- return ret;
- },
-
- has: function( target ) {
- var targets = jQuery( target );
- return this.filter(function() {
- for ( var i = 0, l = targets.length; i < l; i++ ) {
- if ( jQuery.contains( this, targets[i] ) ) {
- return true;
- }
- }
- });
- },
-
- not: function( selector ) {
- return this.pushStack( winnow(this, selector, false), "not", selector);
- },
-
- filter: function( selector ) {
- return this.pushStack( winnow(this, selector, true), "filter", selector );
- },
-
- is: function( selector ) {
- return !!selector && (
- typeof selector === "string" ?
- // If this is a positional selector, check membership in the returned set
- // so $("p:first").is("p:last") won't return true for a doc with two "p".
- POS.test( selector ) ?
- jQuery( selector, this.context ).index( this[0] ) >= 0 :
- jQuery.filter( selector, this ).length > 0 :
- this.filter( selector ).length > 0 );
- },
-
- closest: function( selectors, context ) {
- var ret = [], i, l, cur = this[0];
-
- // Array (deprecated as of jQuery 1.7)
- if ( jQuery.isArray( selectors ) ) {
- var level = 1;
-
- while ( cur && cur.ownerDocument && cur !== context ) {
- for ( i = 0; i < selectors.length; i++ ) {
-
- if ( jQuery( cur ).is( selectors[ i ] ) ) {
- ret.push({ selector: selectors[ i ], elem: cur, level: level });
- }
- }
-
- cur = cur.parentNode;
- level++;
- }
-
- return ret;
- }
-
- // String
- var pos = POS.test( selectors ) || typeof selectors !== "string" ?
- jQuery( selectors, context || this.context ) :
- 0;
-
- for ( i = 0, l = this.length; i < l; i++ ) {
- cur = this[i];
-
- while ( cur ) {
- if ( pos ? pos.index(cur) > -1 : jQuery.find.matchesSelector(cur, selectors) ) {
- ret.push( cur );
- break;
-
- } else {
- cur = cur.parentNode;
- if ( !cur || !cur.ownerDocument || cur === context || cur.nodeType === 11 ) {
- break;
- }
- }
- }
- }
-
- ret = ret.length > 1 ? jQuery.unique( ret ) : ret;
-
- return this.pushStack( ret, "closest", selectors );
- },
-
- // Determine the position of an element within
- // the matched set of elements
- index: function( elem ) {
-
- // No argument, return index in parent
- if ( !elem ) {
- return ( this[0] && this[0].parentNode ) ? this.prevAll().length : -1;
- }
-
- // index in selector
- if ( typeof elem === "string" ) {
- return jQuery.inArray( this[0], jQuery( elem ) );
- }
-
- // Locate the position of the desired element
- return jQuery.inArray(
- // If it receives a jQuery object, the first element is used
- elem.jquery ? elem[0] : elem, this );
- },
-
- add: function( selector, context ) {
- var set = typeof selector === "string" ?
- jQuery( selector, context ) :
- jQuery.makeArray( selector && selector.nodeType ? [ selector ] : selector ),
- all = jQuery.merge( this.get(), set );
-
- return this.pushStack( isDisconnected( set[0] ) || isDisconnected( all[0] ) ?
- all :
- jQuery.unique( all ) );
- },
-
- andSelf: function() {
- return this.add( this.prevObject );
- }
-});
-
-// A painfully simple check to see if an element is disconnected
-// from a document (should be improved, where feasible).
-function isDisconnected( node ) {
- return !node || !node.parentNode || node.parentNode.nodeType === 11;
-}
-
-jQuery.each({
- parent: function( elem ) {
- var parent = elem.parentNode;
- return parent && parent.nodeType !== 11 ? parent : null;
- },
- parents: function( elem ) {
- return jQuery.dir( elem, "parentNode" );
- },
- parentsUntil: function( elem, i, until ) {
- return jQuery.dir( elem, "parentNode", until );
- },
- next: function( elem ) {
- return jQuery.nth( elem, 2, "nextSibling" );
- },
- prev: function( elem ) {
- return jQuery.nth( elem, 2, "previousSibling" );
- },
- nextAll: function( elem ) {
- return jQuery.dir( elem, "nextSibling" );
- },
- prevAll: function( elem ) {
- return jQuery.dir( elem, "previousSibling" );
- },
- nextUntil: function( elem, i, until ) {
- return jQuery.dir( elem, "nextSibling", until );
- },
- prevUntil: function( elem, i, until ) {
- return jQuery.dir( elem, "previousSibling", until );
- },
- siblings: function( elem ) {
- return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem );
- },
- children: function( elem ) {
- return jQuery.sibling( elem.firstChild );
- },
- contents: function( elem ) {
- return jQuery.nodeName( elem, "iframe" ) ?
- elem.contentDocument || elem.contentWindow.document :
- jQuery.makeArray( elem.childNodes );
- }
-}, function( name, fn ) {
- jQuery.fn[ name ] = function( until, selector ) {
- var ret = jQuery.map( this, fn, until );
-
- if ( !runtil.test( name ) ) {
- selector = until;
- }
-
- if ( selector && typeof selector === "string" ) {
- ret = jQuery.filter( selector, ret );
- }
-
- ret = this.length > 1 && !guaranteedUnique[ name ] ? jQuery.unique( ret ) : ret;
-
- if ( (this.length > 1 || rmultiselector.test( selector )) && rparentsprev.test( name ) ) {
- ret = ret.reverse();
- }
-
- return this.pushStack( ret, name, slice.call( arguments ).join(",") );
- };
-});
-
-jQuery.extend({
- filter: function( expr, elems, not ) {
- if ( not ) {
- expr = ":not(" + expr + ")";
- }
-
- return elems.length === 1 ?
- jQuery.find.matchesSelector(elems[0], expr) ? [ elems[0] ] : [] :
- jQuery.find.matches(expr, elems);
- },
-
- dir: function( elem, dir, until ) {
- var matched = [],
- cur = elem[ dir ];
-
- while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) {
- if ( cur.nodeType === 1 ) {
- matched.push( cur );
- }
- cur = cur[dir];
- }
- return matched;
- },
-
- nth: function( cur, result, dir, elem ) {
- result = result || 1;
- var num = 0;
-
- for ( ; cur; cur = cur[dir] ) {
- if ( cur.nodeType === 1 && ++num === result ) {
- break;
- }
- }
-
- return cur;
- },
-
- sibling: function( n, elem ) {
- var r = [];
-
- for ( ; n; n = n.nextSibling ) {
- if ( n.nodeType === 1 && n !== elem ) {
- r.push( n );
- }
- }
-
- return r;
- }
-});
-
-// Implement the identical functionality for filter and not
-function winnow( elements, qualifier, keep ) {
-
- // Can't pass null or undefined to indexOf in Firefox 4
- // Set to 0 to skip string check
- qualifier = qualifier || 0;
-
- if ( jQuery.isFunction( qualifier ) ) {
- return jQuery.grep(elements, function( elem, i ) {
- var retVal = !!qualifier.call( elem, i, elem );
- return retVal === keep;
- });
-
- } else if ( qualifier.nodeType ) {
- return jQuery.grep(elements, function( elem, i ) {
- return ( elem === qualifier ) === keep;
- });
-
- } else if ( typeof qualifier === "string" ) {
- var filtered = jQuery.grep(elements, function( elem ) {
- return elem.nodeType === 1;
- });
-
- if ( isSimple.test( qualifier ) ) {
- return jQuery.filter(qualifier, filtered, !keep);
- } else {
- qualifier = jQuery.filter( qualifier, filtered );
- }
- }
-
- return jQuery.grep(elements, function( elem, i ) {
- return ( jQuery.inArray( elem, qualifier ) >= 0 ) === keep;
- });
-}
-
-
-
-
-function createSafeFragment( document ) {
- var list = nodeNames.split( "|" ),
- safeFrag = document.createDocumentFragment();
-
- if ( safeFrag.createElement ) {
- while ( list.length ) {
- safeFrag.createElement(
- list.pop()
- );
- }
- }
- return safeFrag;
-}
-
-var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" +
- "header|hgroup|mark|meter|nav|output|progress|section|summary|time|video",
- rinlinejQuery = / jQuery\d+="(?:\d+|null)"/g,
- rleadingWhitespace = /^\s+/,
- rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/ig,
- rtagName = /<([\w:]+)/,
- rtbody = /<tbody/i,
- rhtml = /<|&#?\w+;/,
- rnoInnerhtml = /<(?:script|style)/i,
- rnocache = /<(?:script|object|embed|option|style)/i,
- rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"),
- // checked="checked" or checked
- rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
- rscriptType = /\/(java|ecma)script/i,
- rcleanScript = /^\s*<!(?:\[CDATA\[|\-\-)/,
- wrapMap = {
- option: [ 1, "<select multiple='multiple'>", "</select>" ],
- legend: [ 1, "<fieldset>", "</fieldset>" ],
- thead: [ 1, "<table>", "</table>" ],
- tr: [ 2, "<table><tbody>", "</tbody></table>" ],
- td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
- col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ],
- area: [ 1, "<map>", "</map>" ],
- _default: [ 0, "", "" ]
- },
- safeFragment = createSafeFragment( document );
-
-wrapMap.optgroup = wrapMap.option;
-wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
-wrapMap.th = wrapMap.td;
-
-// IE can't serialize <link> and <script> tags normally
-if ( !jQuery.support.htmlSerialize ) {
- wrapMap._default = [ 1, "div<div>", "</div>" ];
-}
-
-jQuery.fn.extend({
- text: function( value ) {
- return jQuery.access( this, function( value ) {
- return value === undefined ?
- jQuery.text( this ) :
- this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) );
- }, null, value, arguments.length );
- },
-
- wrapAll: function( html ) {
- if ( jQuery.isFunction( html ) ) {
- return this.each(function(i) {
- jQuery(this).wrapAll( html.call(this, i) );
- });
- }
-
- if ( this[0] ) {
- // The elements to wrap the target around
- var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true);
-
- if ( this[0].parentNode ) {
- wrap.insertBefore( this[0] );
- }
-
- wrap.map(function() {
- var elem = this;
-
- while ( elem.firstChild && elem.firstChild.nodeType === 1 ) {
- elem = elem.firstChild;
- }
-
- return elem;
- }).append( this );
- }
-
- return this;
- },
-
- wrapInner: function( html ) {
- if ( jQuery.isFunction( html ) ) {
- return this.each(function(i) {
- jQuery(this).wrapInner( html.call(this, i) );
- });
- }
-
- return this.each(function() {
- var self = jQuery( this ),
- contents = self.contents();
-
- if ( contents.length ) {
- contents.wrapAll( html );
-
- } else {
- self.append( html );
- }
- });
- },
-
- wrap: function( html ) {
- var isFunction = jQuery.isFunction( html );
-
- return this.each(function(i) {
- jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html );
- });
- },
-
- unwrap: function() {
- return this.parent().each(function() {
- if ( !jQuery.nodeName( this, "body" ) ) {
- jQuery( this ).replaceWith( this.childNodes );
- }
- }).end();
- },
-
- append: function() {
- return this.domManip(arguments, true, function( elem ) {
- if ( this.nodeType === 1 ) {
- this.appendChild( elem );
- }
- });
- },
-
- prepend: function() {
- return this.domManip(arguments, true, function( elem ) {
- if ( this.nodeType === 1 ) {
- this.insertBefore( elem, this.firstChild );
- }
- });
- },
-
- before: function() {
- if ( this[0] && this[0].parentNode ) {
- return this.domManip(arguments, false, function( elem ) {
- this.parentNode.insertBefore( elem, this );
- });
- } else if ( arguments.length ) {
- var set = jQuery.clean( arguments );
- set.push.apply( set, this.toArray() );
- return this.pushStack( set, "before", arguments );
- }
- },
-
- after: function() {
- if ( this[0] && this[0].parentNode ) {
- return this.domManip(arguments, false, function( elem ) {
- this.parentNode.insertBefore( elem, this.nextSibling );
- });
- } else if ( arguments.length ) {
- var set = this.pushStack( this, "after", arguments );
- set.push.apply( set, jQuery.clean(arguments) );
- return set;
- }
- },
-
- // keepData is for internal use only--do not document
- remove: function( selector, keepData ) {
- for ( var i = 0, elem; (elem = this[i]) != null; i++ ) {
- if ( !selector || jQuery.filter( selector, [ elem ] ).length ) {
- if ( !keepData && elem.nodeType === 1 ) {
- jQuery.cleanData( elem.getElementsByTagName("*") );
- jQuery.cleanData( [ elem ] );
- }
-
- if ( elem.parentNode ) {
- elem.parentNode.removeChild( elem );
- }
- }
- }
-
- return this;
- },
-
- empty: function() {
- for ( var i = 0, elem; (elem = this[i]) != null; i++ ) {
- // Remove element nodes and prevent memory leaks
- if ( elem.nodeType === 1 ) {
- jQuery.cleanData( elem.getElementsByTagName("*") );
- }
-
- // Remove any remaining nodes
- while ( elem.firstChild ) {
- elem.removeChild( elem.firstChild );
- }
- }
-
- return this;
- },
-
- clone: function( dataAndEvents, deepDataAndEvents ) {
- dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
- deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
-
- return this.map( function () {
- return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
- });
- },
-
- html: function( value ) {
- return jQuery.access( this, function( value ) {
- var elem = this[0] || {},
- i = 0,
- l = this.length;
-
- if ( value === undefined ) {
- return elem.nodeType === 1 ?
- elem.innerHTML.replace( rinlinejQuery, "" ) :
- null;
- }
-
-
- if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
- ( jQuery.support.leadingWhitespace || !rleadingWhitespace.test( value ) ) &&
- !wrapMap[ ( rtagName.exec( value ) || ["", ""] )[1].toLowerCase() ] ) {
-
- value = value.replace( rxhtmlTag, "<$1></$2>" );
-
- try {
- for (; i < l; i++ ) {
- // Remove element nodes and prevent memory leaks
- elem = this[i] || {};
- if ( elem.nodeType === 1 ) {
- jQuery.cleanData( elem.getElementsByTagName( "*" ) );
- elem.innerHTML = value;
- }
- }
-
- elem = 0;
-
- // If using innerHTML throws an exception, use the fallback method
- } catch(e) {}
- }
-
- if ( elem ) {
- this.empty().append( value );
- }
- }, null, value, arguments.length );
- },
-
- replaceWith: function( value ) {
- if ( this[0] && this[0].parentNode ) {
- // Make sure that the elements are removed from the DOM before they are inserted
- // this can help fix replacing a parent with child elements
- if ( jQuery.isFunction( value ) ) {
- return this.each(function(i) {
- var self = jQuery(this), old = self.html();
- self.replaceWith( value.call( this, i, old ) );
- });
- }
-
- if ( typeof value !== "string" ) {
- value = jQuery( value ).detach();
- }
-
- return this.each(function() {
- var next = this.nextSibling,
- parent = this.parentNode;
-
- jQuery( this ).remove();
-
- if ( next ) {
- jQuery(next).before( value );
- } else {
- jQuery(parent).append( value );
- }
- });
- } else {
- return this.length ?
- this.pushStack( jQuery(jQuery.isFunction(value) ? value() : value), "replaceWith", value ) :
- this;
- }
- },
-
- detach: function( selector ) {
- return this.remove( selector, true );
- },
-
- domManip: function( args, table, callback ) {
- var results, first, fragment, parent,
- value = args[0],
- scripts = [];
-
- // We can't cloneNode fragments that contain checked, in WebKit
- if ( !jQuery.support.checkClone && arguments.length === 3 && typeof value === "string" && rchecked.test( value ) ) {
- return this.each(function() {
- jQuery(this).domManip( args, table, callback, true );
- });
- }
-
- if ( jQuery.isFunction(value) ) {
- return this.each(function(i) {
- var self = jQuery(this);
- args[0] = value.call(this, i, table ? self.html() : undefined);
- self.domManip( args, table, callback );
- });
- }
-
- if ( this[0] ) {
- parent = value && value.parentNode;
-
- // If we're in a fragment, just use that instead of building a new one
- if ( jQuery.support.parentNode && parent && parent.nodeType === 11 && parent.childNodes.length === this.length ) {
- results = { fragment: parent };
-
- } else {
- results = jQuery.buildFragment( args, this, scripts );
- }
-
- fragment = results.fragment;
-
- if ( fragment.childNodes.length === 1 ) {
- first = fragment = fragment.firstChild;
- } else {
- first = fragment.firstChild;
- }
-
- if ( first ) {
- table = table && jQuery.nodeName( first, "tr" );
-
- for ( var i = 0, l = this.length, lastIndex = l - 1; i < l; i++ ) {
- callback.call(
- table ?
- root(this[i], first) :
- this[i],
- // Make sure that we do not leak memory by inadvertently discarding
- // the original fragment (which might have attached data) instead of
- // using it; in addition, use the original fragment object for the last
- // item instead of first because it can end up being emptied incorrectly
- // in certain situations (Bug #8070).
- // Fragments from the fragment cache must always be cloned and never used
- // in place.
- results.cacheable || ( l > 1 && i < lastIndex ) ?
- jQuery.clone( fragment, true, true ) :
- fragment
- );
- }
- }
-
- if ( scripts.length ) {
- jQuery.each( scripts, function( i, elem ) {
- if ( elem.src ) {
- jQuery.ajax({
- type: "GET",
- global: false,
- url: elem.src,
- async: false,
- dataType: "script"
- });
- } else {
- jQuery.globalEval( ( elem.text || elem.textContent || elem.innerHTML || "" ).replace( rcleanScript, "/*$0*/" ) );
- }
-
- if ( elem.parentNode ) {
- elem.parentNode.removeChild( elem );
- }
- });
- }
- }
-
- return this;
- }
-});
-
-function root( elem, cur ) {
- return jQuery.nodeName(elem, "table") ?
- (elem.getElementsByTagName("tbody")[0] ||
- elem.appendChild(elem.ownerDocument.createElement("tbody"))) :
- elem;
-}
-
-function cloneCopyEvent( src, dest ) {
-
- if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) {
- return;
- }
-
- var type, i, l,
- oldData = jQuery._data( src ),
- curData = jQuery._data( dest, oldData ),
- events = oldData.events;
-
- if ( events ) {
- delete curData.handle;
- curData.events = {};
-
- for ( type in events ) {
- for ( i = 0, l = events[ type ].length; i < l; i++ ) {
- jQuery.event.add( dest, type, events[ type ][ i ] );
- }
- }
- }
-
- // make the cloned public data object a copy from the original
- if ( curData.data ) {
- curData.data = jQuery.extend( {}, curData.data );
- }
-}
-
-function cloneFixAttributes( src, dest ) {
- var nodeName;
-
- // We do not need to do anything for non-Elements
- if ( dest.nodeType !== 1 ) {
- return;
- }
-
- // clearAttributes removes the attributes, which we don't want,
- // but also removes the attachEvent events, which we *do* want
- if ( dest.clearAttributes ) {
- dest.clearAttributes();
- }
-
- // mergeAttributes, in contrast, only merges back on the
- // original attributes, not the events
- if ( dest.mergeAttributes ) {
- dest.mergeAttributes( src );
- }
-
- nodeName = dest.nodeName.toLowerCase();
-
- // IE6-8 fail to clone children inside object elements that use
- // the proprietary classid attribute value (rather than the type
- // attribute) to identify the type of content to display
- if ( nodeName === "object" ) {
- dest.outerHTML = src.outerHTML;
-
- } else if ( nodeName === "input" && (src.type === "checkbox" || src.type === "radio") ) {
- // IE6-8 fails to persist the checked state of a cloned checkbox
- // or radio button. Worse, IE6-7 fail to give the cloned element
- // a checked appearance if the defaultChecked value isn't also set
- if ( src.checked ) {
- dest.defaultChecked = dest.checked = src.checked;
- }
-
- // IE6-7 get confused and end up setting the value of a cloned
- // checkbox/radio button to an empty string instead of "on"
- if ( dest.value !== src.value ) {
- dest.value = src.value;
- }
-
- // IE6-8 fails to return the selected option to the default selected
- // state when cloning options
- } else if ( nodeName === "option" ) {
- dest.selected = src.defaultSelected;
-
- // IE6-8 fails to set the defaultValue to the correct value when
- // cloning other types of input fields
- } else if ( nodeName === "input" || nodeName === "textarea" ) {
- dest.defaultValue = src.defaultValue;
-
- // IE blanks contents when cloning scripts
- } else if ( nodeName === "script" && dest.text !== src.text ) {
- dest.text = src.text;
- }
-
- // Event data gets referenced instead of copied if the expando
- // gets copied too
- dest.removeAttribute( jQuery.expando );
-
- // Clear flags for bubbling special change/submit events, they must
- // be reattached when the newly cloned events are first activated
- dest.removeAttribute( "_submit_attached" );
- dest.removeAttribute( "_change_attached" );
-}
-
-jQuery.buildFragment = function( args, nodes, scripts ) {
- var fragment, cacheable, cacheresults, doc,
- first = args[ 0 ];
-
- // nodes may contain either an explicit document object,
- // a jQuery collection or context object.
- // If nodes[0] contains a valid object to assign to doc
- if ( nodes && nodes[0] ) {
- doc = nodes[0].ownerDocument || nodes[0];
- }
-
- // Ensure that an attr object doesn't incorrectly stand in as a document object
- // Chrome and Firefox seem to allow this to occur and will throw exception
- // Fixes #8950
- if ( !doc.createDocumentFragment ) {
- doc = document;
- }
-
- // Only cache "small" (1/2 KB) HTML strings that are associated with the main document
- // Cloning options loses the selected state, so don't cache them
- // IE 6 doesn't like it when you put <object> or <embed> elements in a fragment
- // Also, WebKit does not clone 'checked' attributes on cloneNode, so don't cache
- // Lastly, IE6,7,8 will not correctly reuse cached fragments that were created from unknown elems #10501
- if ( args.length === 1 && typeof first === "string" && first.length < 512 && doc === document &&
- first.charAt(0) === "<" && !rnocache.test( first ) &&
- (jQuery.support.checkClone || !rchecked.test( first )) &&
- (jQuery.support.html5Clone || !rnoshimcache.test( first )) ) {
-
- cacheable = true;
-
- cacheresults = jQuery.fragments[ first ];
- if ( cacheresults && cacheresults !== 1 ) {
- fragment = cacheresults;
- }
- }
-
- if ( !fragment ) {
- fragment = doc.createDocumentFragment();
- jQuery.clean( args, doc, fragment, scripts );
- }
-
- if ( cacheable ) {
- jQuery.fragments[ first ] = cacheresults ? fragment : 1;
- }
-
- return { fragment: fragment, cacheable: cacheable };
-};
-
-jQuery.fragments = {};
-
-jQuery.each({
- appendTo: "append",
- prependTo: "prepend",
- insertBefore: "before",
- insertAfter: "after",
- replaceAll: "replaceWith"
-}, function( name, original ) {
- jQuery.fn[ name ] = function( selector ) {
- var ret = [],
- insert = jQuery( selector ),
- parent = this.length === 1 && this[0].parentNode;
-
- if ( parent && parent.nodeType === 11 && parent.childNodes.length === 1 && insert.length === 1 ) {
- insert[ original ]( this[0] );
- return this;
-
- } else {
- for ( var i = 0, l = insert.length; i < l; i++ ) {
- var elems = ( i > 0 ? this.clone(true) : this ).get();
- jQuery( insert[i] )[ original ]( elems );
- ret = ret.concat( elems );
- }
-
- return this.pushStack( ret, name, insert.selector );
- }
- };
-});
-
-function getAll( elem ) {
- if ( typeof elem.getElementsByTagName !== "undefined" ) {
- return elem.getElementsByTagName( "*" );
-
- } else if ( typeof elem.querySelectorAll !== "undefined" ) {
- return elem.querySelectorAll( "*" );
-
- } else {
- return [];
- }
-}
-
-// Used in clean, fixes the defaultChecked property
-function fixDefaultChecked( elem ) {
- if ( elem.type === "checkbox" || elem.type === "radio" ) {
- elem.defaultChecked = elem.checked;
- }
-}
-// Finds all inputs and passes them to fixDefaultChecked
-function findInputs( elem ) {
- var nodeName = ( elem.nodeName || "" ).toLowerCase();
- if ( nodeName === "input" ) {
- fixDefaultChecked( elem );
- // Skip scripts, get other children
- } else if ( nodeName !== "script" && typeof elem.getElementsByTagName !== "undefined" ) {
- jQuery.grep( elem.getElementsByTagName("input"), fixDefaultChecked );
- }
-}
-
-// Derived From: http://www.iecss.com/shimprove/javascript/shimprove.1-0-1.js
-function shimCloneNode( elem ) {
- var div = document.createElement( "div" );
- safeFragment.appendChild( div );
-
- div.innerHTML = elem.outerHTML;
- return div.firstChild;
-}
-
-jQuery.extend({
- clone: function( elem, dataAndEvents, deepDataAndEvents ) {
- var srcElements,
- destElements,
- i,
- // IE<=8 does not properly clone detached, unknown element nodes
- clone = jQuery.support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ?
- elem.cloneNode( true ) :
- shimCloneNode( elem );
-
- if ( (!jQuery.support.noCloneEvent || !jQuery.support.noCloneChecked) &&
- (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) {
- // IE copies events bound via attachEvent when using cloneNode.
- // Calling detachEvent on the clone will also remove the events
- // from the original. In order to get around this, we use some
- // proprietary methods to clear the events. Thanks to MooTools
- // guys for this hotness.
-
- cloneFixAttributes( elem, clone );
-
- // Using Sizzle here is crazy slow, so we use getElementsByTagName instead
- srcElements = getAll( elem );
- destElements = getAll( clone );
-
- // Weird iteration because IE will replace the length property
- // with an element if you are cloning the body and one of the
- // elements on the page has a name or id of "length"
- for ( i = 0; srcElements[i]; ++i ) {
- // Ensure that the destination node is not null; Fixes #9587
- if ( destElements[i] ) {
- cloneFixAttributes( srcElements[i], destElements[i] );
- }
- }
- }
-
- // Copy the events from the original to the clone
- if ( dataAndEvents ) {
- cloneCopyEvent( elem, clone );
-
- if ( deepDataAndEvents ) {
- srcElements = getAll( elem );
- destElements = getAll( clone );
-
- for ( i = 0; srcElements[i]; ++i ) {
- cloneCopyEvent( srcElements[i], destElements[i] );
- }
- }
- }
-
- srcElements = destElements = null;
-
- // Return the cloned set
- return clone;
- },
-
- clean: function( elems, context, fragment, scripts ) {
- var checkScriptType, script, j,
- ret = [];
-
- context = context || document;
-
- // !context.createElement fails in IE with an error but returns typeof 'object'
- if ( typeof context.createElement === "undefined" ) {
- context = context.ownerDocument || context[0] && context[0].ownerDocument || document;
- }
-
- for ( var i = 0, elem; (elem = elems[i]) != null; i++ ) {
- if ( typeof elem === "number" ) {
- elem += "";
- }
-
- if ( !elem ) {
- continue;
- }
-
- // Convert html string into DOM nodes
- if ( typeof elem === "string" ) {
- if ( !rhtml.test( elem ) ) {
- elem = context.createTextNode( elem );
- } else {
- // Fix "XHTML"-style tags in all browsers
- elem = elem.replace(rxhtmlTag, "<$1></$2>");
-
- // Trim whitespace, otherwise indexOf won't work as expected
- var tag = ( rtagName.exec( elem ) || ["", ""] )[1].toLowerCase(),
- wrap = wrapMap[ tag ] || wrapMap._default,
- depth = wrap[0],
- div = context.createElement("div"),
- safeChildNodes = safeFragment.childNodes,
- remove;
-
- // Append wrapper element to unknown element safe doc fragment
- if ( context === document ) {
- // Use the fragment we've already created for this document
- safeFragment.appendChild( div );
- } else {
- // Use a fragment created with the owner document
- createSafeFragment( context ).appendChild( div );
- }
-
- // Go to html and back, then peel off extra wrappers
- div.innerHTML = wrap[1] + elem + wrap[2];
-
- // Move to the right depth
- while ( depth-- ) {
- div = div.lastChild;
- }
-
- // Remove IE's autoinserted <tbody> from table fragments
- if ( !jQuery.support.tbody ) {
-
- // String was a <table>, *may* have spurious <tbody>
- var hasBody = rtbody.test(elem),
- tbody = tag === "table" && !hasBody ?
- div.firstChild && div.firstChild.childNodes :
-
- // String was a bare <thead> or <tfoot>
- wrap[1] === "<table>" && !hasBody ?
- div.childNodes :
- [];
-
- for ( j = tbody.length - 1; j >= 0 ; --j ) {
- if ( jQuery.nodeName( tbody[ j ], "tbody" ) && !tbody[ j ].childNodes.length ) {
- tbody[ j ].parentNode.removeChild( tbody[ j ] );
- }
- }
- }
-
- // IE completely kills leading whitespace when innerHTML is used
- if ( !jQuery.support.leadingWhitespace && rleadingWhitespace.test( elem ) ) {
- div.insertBefore( context.createTextNode( rleadingWhitespace.exec(elem)[0] ), div.firstChild );
- }
-
- elem = div.childNodes;
-
- // Clear elements from DocumentFragment (safeFragment or otherwise)
- // to avoid hoarding elements. Fixes #11356
- if ( div ) {
- div.parentNode.removeChild( div );
-
- // Guard against -1 index exceptions in FF3.6
- if ( safeChildNodes.length > 0 ) {
- remove = safeChildNodes[ safeChildNodes.length - 1 ];
-
- if ( remove && remove.parentNode ) {
- remove.parentNode.removeChild( remove );
- }
- }
- }
- }
- }
-
- // Resets defaultChecked for any radios and checkboxes
- // about to be appended to the DOM in IE 6/7 (#8060)
- var len;
- if ( !jQuery.support.appendChecked ) {
- if ( elem[0] && typeof (len = elem.length) === "number" ) {
- for ( j = 0; j < len; j++ ) {
- findInputs( elem[j] );
- }
- } else {
- findInputs( elem );
- }
- }
-
- if ( elem.nodeType ) {
- ret.push( elem );
- } else {
- ret = jQuery.merge( ret, elem );
- }
- }
-
- if ( fragment ) {
- checkScriptType = function( elem ) {
- return !elem.type || rscriptType.test( elem.type );
- };
- for ( i = 0; ret[i]; i++ ) {
- script = ret[i];
- if ( scripts && jQuery.nodeName( script, "script" ) && (!script.type || rscriptType.test( script.type )) ) {
- scripts.push( script.parentNode ? script.parentNode.removeChild( script ) : script );
-
- } else {
- if ( script.nodeType === 1 ) {
- var jsTags = jQuery.grep( script.getElementsByTagName( "script" ), checkScriptType );
-
- ret.splice.apply( ret, [i + 1, 0].concat( jsTags ) );
- }
- fragment.appendChild( script );
- }
- }
- }
-
- return ret;
- },
-
- cleanData: function( elems ) {
- var data, id,
- cache = jQuery.cache,
- special = jQuery.event.special,
- deleteExpando = jQuery.support.deleteExpando;
-
- for ( var i = 0, elem; (elem = elems[i]) != null; i++ ) {
- if ( elem.nodeName && jQuery.noData[elem.nodeName.toLowerCase()] ) {
- continue;
- }
-
- id = elem[ jQuery.expando ];
-
- if ( id ) {
- data = cache[ id ];
-
- if ( data && data.events ) {
- for ( var type in data.events ) {
- if ( special[ type ] ) {
- jQuery.event.remove( elem, type );
-
- // This is a shortcut to avoid jQuery.event.remove's overhead
- } else {
- jQuery.removeEvent( elem, type, data.handle );
- }
- }
-
- // Null the DOM reference to avoid IE6/7/8 leak (#7054)
- if ( data.handle ) {
- data.handle.elem = null;
- }
- }
-
- if ( deleteExpando ) {
- delete elem[ jQuery.expando ];
-
- } else if ( elem.removeAttribute ) {
- elem.removeAttribute( jQuery.expando );
- }
-
- delete cache[ id ];
- }
- }
- }
-});
-
-
-
-
-var ralpha = /alpha\([^)]*\)/i,
- ropacity = /opacity=([^)]*)/,
- // fixed for IE9, see #8346
- rupper = /([A-Z]|^ms)/g,
- rnum = /^[\-+]?(?:\d*\.)?\d+$/i,
- rnumnonpx = /^-?(?:\d*\.)?\d+(?!px)[^\d\s]+$/i,
- rrelNum = /^([\-+])=([\-+.\de]+)/,
- rmargin = /^margin/,
-
- cssShow = { position: "absolute", visibility: "hidden", display: "block" },
-
- // order is important!
- cssExpand = [ "Top", "Right", "Bottom", "Left" ],
-
- curCSS,
-
- getComputedStyle,
- currentStyle;
-
-jQuery.fn.css = function( name, value ) {
- return jQuery.access( this, function( elem, name, value ) {
- return value !== undefined ?
- jQuery.style( elem, name, value ) :
- jQuery.css( elem, name );
- }, name, value, arguments.length > 1 );
-};
-
-jQuery.extend({
- // Add in style property hooks for overriding the default
- // behavior of getting and setting a style property
- cssHooks: {
- opacity: {
- get: function( elem, computed ) {
- if ( computed ) {
- // We should always get a number back from opacity
- var ret = curCSS( elem, "opacity" );
- return ret === "" ? "1" : ret;
-
- } else {
- return elem.style.opacity;
- }
- }
- }
- },
-
- // Exclude the following css properties to add px
- cssNumber: {
- "fillOpacity": true,
- "fontWeight": true,
- "lineHeight": true,
- "opacity": true,
- "orphans": true,
- "widows": true,
- "zIndex": true,
- "zoom": true
- },
-
- // Add in properties whose names you wish to fix before
- // setting or getting the value
- cssProps: {
- // normalize float css property
- "float": jQuery.support.cssFloat ? "cssFloat" : "styleFloat"
- },
-
- // Get and set the style property on a DOM Node
- style: function( elem, name, value, extra ) {
- // Don't set styles on text and comment nodes
- if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
- return;
- }
-
- // Make sure that we're working with the right name
- var ret, type, origName = jQuery.camelCase( name ),
- style = elem.style, hooks = jQuery.cssHooks[ origName ];
-
- name = jQuery.cssProps[ origName ] || origName;
-
- // Check if we're setting a value
- if ( value !== undefined ) {
- type = typeof value;
-
- // convert relative number strings (+= or -=) to relative numbers. #7345
- if ( type === "string" && (ret = rrelNum.exec( value )) ) {
- value = ( +( ret[1] + 1) * +ret[2] ) + parseFloat( jQuery.css( elem, name ) );
- // Fixes bug #9237
- type = "number";
- }
-
- // Make sure that NaN and null values aren't set. See: #7116
- if ( value == null || type === "number" && isNaN( value ) ) {
- return;
- }
-
- // If a number was passed in, add 'px' to the (except for certain CSS properties)
- if ( type === "number" && !jQuery.cssNumber[ origName ] ) {
- value += "px";
- }
-
- // If a hook was provided, use that value, otherwise just set the specified value
- if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value )) !== undefined ) {
- // Wrapped to prevent IE from throwing errors when 'invalid' values are provided
- // Fixes bug #5509
- try {
- style[ name ] = value;
- } catch(e) {}
- }
-
- } else {
- // If a hook was provided get the non-computed value from there
- if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) {
- return ret;
- }
-
- // Otherwise just get the value from the style object
- return style[ name ];
- }
- },
-
- css: function( elem, name, extra ) {
- var ret, hooks;
-
- // Make sure that we're working with the right name
- name = jQuery.camelCase( name );
- hooks = jQuery.cssHooks[ name ];
- name = jQuery.cssProps[ name ] || name;
-
- // cssFloat needs a special treatment
- if ( name === "cssFloat" ) {
- name = "float";
- }
-
- // If a hook was provided get the computed value from there
- if ( hooks && "get" in hooks && (ret = hooks.get( elem, true, extra )) !== undefined ) {
- return ret;
-
- // Otherwise, if a way to get the computed value exists, use that
- } else if ( curCSS ) {
- return curCSS( elem, name );
- }
- },
-
- // A method for quickly swapping in/out CSS properties to get correct calculations
- swap: function( elem, options, callback ) {
- var old = {},
- ret, name;
-
- // Remember the old values, and insert the new ones
- for ( name in options ) {
- old[ name ] = elem.style[ name ];
- elem.style[ name ] = options[ name ];
- }
-
- ret = callback.call( elem );
-
- // Revert the old values
- for ( name in options ) {
- elem.style[ name ] = old[ name ];
- }
-
- return ret;
- }
-});
-
-// DEPRECATED in 1.3, Use jQuery.css() instead
-jQuery.curCSS = jQuery.css;
-
-if ( document.defaultView && document.defaultView.getComputedStyle ) {
- getComputedStyle = function( elem, name ) {
- var ret, defaultView, computedStyle, width,
- style = elem.style;
-
- name = name.replace( rupper, "-$1" ).toLowerCase();
-
- if ( (defaultView = elem.ownerDocument.defaultView) &&
- (computedStyle = defaultView.getComputedStyle( elem, null )) ) {
-
- ret = computedStyle.getPropertyValue( name );
- if ( ret === "" && !jQuery.contains( elem.ownerDocument.documentElement, elem ) ) {
- ret = jQuery.style( elem, name );
- }
- }
-
- // A tribute to the "awesome hack by Dean Edwards"
- // WebKit uses "computed value (percentage if specified)" instead of "used value" for margins
- // which is against the CSSOM draft spec: http://dev.w3.org/csswg/cssom/#resolved-values
- if ( !jQuery.support.pixelMargin && computedStyle && rmargin.test( name ) && rnumnonpx.test( ret ) ) {
- width = style.width;
- style.width = ret;
- ret = computedStyle.width;
- style.width = width;
- }
-
- return ret;
- };
-}
-
-if ( document.documentElement.currentStyle ) {
- currentStyle = function( elem, name ) {
- var left, rsLeft, uncomputed,
- ret = elem.currentStyle && elem.currentStyle[ name ],
- style = elem.style;
-
- // Avoid setting ret to empty string here
- // so we don't default to auto
- if ( ret == null && style && (uncomputed = style[ name ]) ) {
- ret = uncomputed;
- }
-
- // From the awesome hack by Dean Edwards
- // http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291
-
- // If we're not dealing with a regular pixel number
- // but a number that has a weird ending, we need to convert it to pixels
- if ( rnumnonpx.test( ret ) ) {
-
- // Remember the original values
- left = style.left;
- rsLeft = elem.runtimeStyle && elem.runtimeStyle.left;
-
- // Put in the new values to get a computed value out
- if ( rsLeft ) {
- elem.runtimeStyle.left = elem.currentStyle.left;
- }
- style.left = name === "fontSize" ? "1em" : ret;
- ret = style.pixelLeft + "px";
-
- // Revert the changed values
- style.left = left;
- if ( rsLeft ) {
- elem.runtimeStyle.left = rsLeft;
- }
- }
-
- return ret === "" ? "auto" : ret;
- };
-}
-
-curCSS = getComputedStyle || currentStyle;
-
-function getWidthOrHeight( elem, name, extra ) {
-
- // Start with offset property
- var val = name === "width" ? elem.offsetWidth : elem.offsetHeight,
- i = name === "width" ? 1 : 0,
- len = 4;
-
- if ( val > 0 ) {
- if ( extra !== "border" ) {
- for ( ; i < len; i += 2 ) {
- if ( !extra ) {
- val -= parseFloat( jQuery.css( elem, "padding" + cssExpand[ i ] ) ) || 0;
- }
- if ( extra === "margin" ) {
- val += parseFloat( jQuery.css( elem, extra + cssExpand[ i ] ) ) || 0;
- } else {
- val -= parseFloat( jQuery.css( elem, "border" + cssExpand[ i ] + "Width" ) ) || 0;
- }
- }
- }
-
- return val + "px";
- }
-
- // Fall back to computed then uncomputed css if necessary
- val = curCSS( elem, name );
- if ( val < 0 || val == null ) {
- val = elem.style[ name ];
- }
-
- // Computed unit is not pixels. Stop here and return.
- if ( rnumnonpx.test(val) ) {
- return val;
- }
-
- // Normalize "", auto, and prepare for extra
- val = parseFloat( val ) || 0;
-
- // Add padding, border, margin
- if ( extra ) {
- for ( ; i < len; i += 2 ) {
- val += parseFloat( jQuery.css( elem, "padding" + cssExpand[ i ] ) ) || 0;
- if ( extra !== "padding" ) {
- val += parseFloat( jQuery.css( elem, "border" + cssExpand[ i ] + "Width" ) ) || 0;
- }
- if ( extra === "margin" ) {
- val += parseFloat( jQuery.css( elem, extra + cssExpand[ i ]) ) || 0;
- }
- }
- }
-
- return val + "px";
-}
-
-jQuery.each([ "height", "width" ], function( i, name ) {
- jQuery.cssHooks[ name ] = {
- get: function( elem, computed, extra ) {
- if ( computed ) {
- if ( elem.offsetWidth !== 0 ) {
- return getWidthOrHeight( elem, name, extra );
- } else {
- return jQuery.swap( elem, cssShow, function() {
- return getWidthOrHeight( elem, name, extra );
- });
- }
- }
- },
-
- set: function( elem, value ) {
- return rnum.test( value ) ?
- value + "px" :
- value;
- }
- };
-});
-
-if ( !jQuery.support.opacity ) {
- jQuery.cssHooks.opacity = {
- get: function( elem, computed ) {
- // IE uses filters for opacity
- return ropacity.test( (computed && elem.currentStyle ? elem.currentStyle.filter : elem.style.filter) || "" ) ?
- ( parseFloat( RegExp.$1 ) / 100 ) + "" :
- computed ? "1" : "";
- },
-
- set: function( elem, value ) {
- var style = elem.style,
- currentStyle = elem.currentStyle,
- opacity = jQuery.isNumeric( value ) ? "alpha(opacity=" + value * 100 + ")" : "",
- filter = currentStyle && currentStyle.filter || style.filter || "";
-
- // IE has trouble with opacity if it does not have layout
- // Force it by setting the zoom level
- style.zoom = 1;
-
- // if setting opacity to 1, and no other filters exist - attempt to remove filter attribute #6652
- if ( value >= 1 && jQuery.trim( filter.replace( ralpha, "" ) ) === "" ) {
-
- // Setting style.filter to null, "" & " " still leave "filter:" in the cssText
- // if "filter:" is present at all, clearType is disabled, we want to avoid this
- // style.removeAttribute is IE Only, but so apparently is this code path...
- style.removeAttribute( "filter" );
-
- // if there there is no filter style applied in a css rule, we are done
- if ( currentStyle && !currentStyle.filter ) {
- return;
- }
- }
-
- // otherwise, set new filter values
- style.filter = ralpha.test( filter ) ?
- filter.replace( ralpha, opacity ) :
- filter + " " + opacity;
- }
- };
-}
-
-jQuery(function() {
- // This hook cannot be added until DOM ready because the support test
- // for it is not run until after DOM ready
- if ( !jQuery.support.reliableMarginRight ) {
- jQuery.cssHooks.marginRight = {
- get: function( elem, computed ) {
- // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
- // Work around by temporarily setting element display to inline-block
- return jQuery.swap( elem, { "display": "inline-block" }, function() {
- if ( computed ) {
- return curCSS( elem, "margin-right" );
- } else {
- return elem.style.marginRight;
- }
- });
- }
- };
- }
-});
-
-if ( jQuery.expr && jQuery.expr.filters ) {
- jQuery.expr.filters.hidden = function( elem ) {
- var width = elem.offsetWidth,
- height = elem.offsetHeight;
-
- return ( width === 0 && height === 0 ) || (!jQuery.support.reliableHiddenOffsets && ((elem.style && elem.style.display) || jQuery.css( elem, "display" )) === "none");
- };
-
- jQuery.expr.filters.visible = function( elem ) {
- return !jQuery.expr.filters.hidden( elem );
- };
-}
-
-// These hooks are used by animate to expand properties
-jQuery.each({
- margin: "",
- padding: "",
- border: "Width"
-}, function( prefix, suffix ) {
-
- jQuery.cssHooks[ prefix + suffix ] = {
- expand: function( value ) {
- var i,
-
- // assumes a single number if not a string
- parts = typeof value === "string" ? value.split(" ") : [ value ],
- expanded = {};
-
- for ( i = 0; i < 4; i++ ) {
- expanded[ prefix + cssExpand[ i ] + suffix ] =
- parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
- }
-
- return expanded;
- }
- };
-});
-
-
-
-
-var r20 = /%20/g,
- rbracket = /\[\]$/,
- rCRLF = /\r?\n/g,
- rhash = /#.*$/,
- rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL
- rinput = /^(?:color|date|datetime|datetime-local|email|hidden|month|number|password|range|search|tel|text|time|url|week)$/i,
- // #7653, #8125, #8152: local protocol detection
- rlocalProtocol = /^(?:about|app|app\-storage|.+\-extension|file|res|widget):$/,
- rnoContent = /^(?:GET|HEAD)$/,
- rprotocol = /^\/\//,
- rquery = /\?/,
- rscript = /<script\b[^<]*(?:(?!<\/script>)<[^<]*)*<\/script>/gi,
- rselectTextarea = /^(?:select|textarea)/i,
- rspacesAjax = /\s+/,
- rts = /([?&])_=[^&]*/,
- rurl = /^([\w\+\.\-]+:)(?:\/\/([^\/?#:]*)(?::(\d+))?)?/,
-
- // Keep a copy of the old load method
- _load = jQuery.fn.load,
-
- /* Prefilters
- * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
- * 2) These are called:
- * - BEFORE asking for a transport
- * - AFTER param serialization (s.data is a string if s.processData is true)
- * 3) key is the dataType
- * 4) the catchall symbol "*" can be used
- * 5) execution will start with transport dataType and THEN continue down to "*" if needed
- */
- prefilters = {},
-
- /* Transports bindings
- * 1) key is the dataType
- * 2) the catchall symbol "*" can be used
- * 3) selection will start with transport dataType and THEN go to "*" if needed
- */
- transports = {},
-
- // Document location
- ajaxLocation,
-
- // Document location segments
- ajaxLocParts,
-
- // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
- allTypes = ["*/"] + ["*"];
-
-// #8138, IE may throw an exception when accessing
-// a field from window.location if document.domain has been set
-try {
- ajaxLocation = location.href;
-} catch( e ) {
- // Use the href attribute of an A element
- // since IE will modify it given document.location
- ajaxLocation = document.createElement( "a" );
- ajaxLocation.href = "";
- ajaxLocation = ajaxLocation.href;
-}
-
-// Segment location into parts
-ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || [];
-
-// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
-function addToPrefiltersOrTransports( structure ) {
-
- // dataTypeExpression is optional and defaults to "*"
- return function( dataTypeExpression, func ) {
-
- if ( typeof dataTypeExpression !== "string" ) {
- func = dataTypeExpression;
- dataTypeExpression = "*";
- }
-
- if ( jQuery.isFunction( func ) ) {
- var dataTypes = dataTypeExpression.toLowerCase().split( rspacesAjax ),
- i = 0,
- length = dataTypes.length,
- dataType,
- list,
- placeBefore;
-
- // For each dataType in the dataTypeExpression
- for ( ; i < length; i++ ) {
- dataType = dataTypes[ i ];
- // We control if we're asked to add before
- // any existing element
- placeBefore = /^\+/.test( dataType );
- if ( placeBefore ) {
- dataType = dataType.substr( 1 ) || "*";
- }
- list = structure[ dataType ] = structure[ dataType ] || [];
- // then we add to the structure accordingly
- list[ placeBefore ? "unshift" : "push" ]( func );
- }
- }
- };
-}
-
-// Base inspection function for prefilters and transports
-function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR,
- dataType /* internal */, inspected /* internal */ ) {
-
- dataType = dataType || options.dataTypes[ 0 ];
- inspected = inspected || {};
-
- inspected[ dataType ] = true;
-
- var list = structure[ dataType ],
- i = 0,
- length = list ? list.length : 0,
- executeOnly = ( structure === prefilters ),
- selection;
-
- for ( ; i < length && ( executeOnly || !selection ); i++ ) {
- selection = list[ i ]( options, originalOptions, jqXHR );
- // If we got redirected to another dataType
- // we try there if executing only and not done already
- if ( typeof selection === "string" ) {
- if ( !executeOnly || inspected[ selection ] ) {
- selection = undefined;
- } else {
- options.dataTypes.unshift( selection );
- selection = inspectPrefiltersOrTransports(
- structure, options, originalOptions, jqXHR, selection, inspected );
- }
- }
- }
- // If we're only executing or nothing was selected
- // we try the catchall dataType if not done already
- if ( ( executeOnly || !selection ) && !inspected[ "*" ] ) {
- selection = inspectPrefiltersOrTransports(
- structure, options, originalOptions, jqXHR, "*", inspected );
- }
- // unnecessary when only executing (prefilters)
- // but it'll be ignored by the caller in that case
- return selection;
-}
-
-// A special extend for ajax options
-// that takes "flat" options (not to be deep extended)
-// Fixes #9887
-function ajaxExtend( target, src ) {
- var key, deep,
- flatOptions = jQuery.ajaxSettings.flatOptions || {};
- for ( key in src ) {
- if ( src[ key ] !== undefined ) {
- ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ];
- }
- }
- if ( deep ) {
- jQuery.extend( true, target, deep );
- }
-}
-
-jQuery.fn.extend({
- load: function( url, params, callback ) {
- if ( typeof url !== "string" && _load ) {
- return _load.apply( this, arguments );
-
- // Don't do a request if no elements are being requested
- } else if ( !this.length ) {
- return this;
- }
-
- var off = url.indexOf( " " );
- if ( off >= 0 ) {
- var selector = url.slice( off, url.length );
- url = url.slice( 0, off );
- }
-
- // Default to a GET request
- var type = "GET";
-
- // If the second parameter was provided
- if ( params ) {
- // If it's a function
- if ( jQuery.isFunction( params ) ) {
- // We assume that it's the callback
- callback = params;
- params = undefined;
-
- // Otherwise, build a param string
- } else if ( typeof params === "object" ) {
- params = jQuery.param( params, jQuery.ajaxSettings.traditional );
- type = "POST";
- }
- }
-
- var self = this;
-
- // Request the remote document
- jQuery.ajax({
- url: url,
- type: type,
- dataType: "html",
- data: params,
- // Complete callback (responseText is used internally)
- complete: function( jqXHR, status, responseText ) {
- // Store the response as specified by the jqXHR object
- responseText = jqXHR.responseText;
- // If successful, inject the HTML into all the matched elements
- if ( jqXHR.isResolved() ) {
- // #4825: Get the actual response in case
- // a dataFilter is present in ajaxSettings
- jqXHR.done(function( r ) {
- responseText = r;
- });
- // See if a selector was specified
- self.html( selector ?
- // Create a dummy div to hold the results
- jQuery("<div>")
- // inject the contents of the document in, removing the scripts
- // to avoid any 'Permission Denied' errors in IE
- .append(responseText.replace(rscript, ""))
-
- // Locate the specified elements
- .find(selector) :
-
- // If not, just inject the full result
- responseText );
- }
-
- if ( callback ) {
- self.each( callback, [ responseText, status, jqXHR ] );
- }
- }
- });
-
- return this;
- },
-
- serialize: function() {
- return jQuery.param( this.serializeArray() );
- },
-
- serializeArray: function() {
- return this.map(function(){
- return this.elements ? jQuery.makeArray( this.elements ) : this;
- })
- .filter(function(){
- return this.name && !this.disabled &&
- ( this.checked || rselectTextarea.test( this.nodeName ) ||
- rinput.test( this.type ) );
- })
- .map(function( i, elem ){
- var val = jQuery( this ).val();
-
- return val == null ?
- null :
- jQuery.isArray( val ) ?
- jQuery.map( val, function( val, i ){
- return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
- }) :
- { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
- }).get();
- }
-});
-
-// Attach a bunch of functions for handling common AJAX events
-jQuery.each( "ajaxStart ajaxStop ajaxComplete ajaxError ajaxSuccess ajaxSend".split( " " ), function( i, o ){
- jQuery.fn[ o ] = function( f ){
- return this.on( o, f );
- };
-});
-
-jQuery.each( [ "get", "post" ], function( i, method ) {
- jQuery[ method ] = function( url, data, callback, type ) {
- // shift arguments if data argument was omitted
- if ( jQuery.isFunction( data ) ) {
- type = type || callback;
- callback = data;
- data = undefined;
- }
-
- return jQuery.ajax({
- type: method,
- url: url,
- data: data,
- success: callback,
- dataType: type
- });
- };
-});
-
-jQuery.extend({
-
- getScript: function( url, callback ) {
- return jQuery.get( url, undefined, callback, "script" );
- },
-
- getJSON: function( url, data, callback ) {
- return jQuery.get( url, data, callback, "json" );
- },
-
- // Creates a full fledged settings object into target
- // with both ajaxSettings and settings fields.
- // If target is omitted, writes into ajaxSettings.
- ajaxSetup: function( target, settings ) {
- if ( settings ) {
- // Building a settings object
- ajaxExtend( target, jQuery.ajaxSettings );
- } else {
- // Extending ajaxSettings
- settings = target;
- target = jQuery.ajaxSettings;
- }
- ajaxExtend( target, settings );
- return target;
- },
-
- ajaxSettings: {
- url: ajaxLocation,
- isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ),
- global: true,
- type: "GET",
- contentType: "application/x-www-form-urlencoded; charset=UTF-8",
- processData: true,
- async: true,
- /*
- timeout: 0,
- data: null,
- dataType: null,
- username: null,
- password: null,
- cache: null,
- traditional: false,
- headers: {},
- */
-
- accepts: {
- xml: "application/xml, text/xml",
- html: "text/html",
- text: "text/plain",
- json: "application/json, text/javascript",
- "*": allTypes
- },
-
- contents: {
- xml: /xml/,
- html: /html/,
- json: /json/
- },
-
- responseFields: {
- xml: "responseXML",
- text: "responseText"
- },
-
- // List of data converters
- // 1) key format is "source_type destination_type" (a single space in-between)
- // 2) the catchall symbol "*" can be used for source_type
- converters: {
-
- // Convert anything to text
- "* text": window.String,
-
- // Text to html (true = no transformation)
- "text html": true,
-
- // Evaluate text as a json expression
- "text json": jQuery.parseJSON,
-
- // Parse text as xml
- "text xml": jQuery.parseXML
- },
-
- // For options that shouldn't be deep extended:
- // you can add your own custom options here if
- // and when you create one that shouldn't be
- // deep extended (see ajaxExtend)
- flatOptions: {
- context: true,
- url: true
- }
- },
-
- ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
- ajaxTransport: addToPrefiltersOrTransports( transports ),
-
- // Main method
- ajax: function( url, options ) {
-
- // If url is an object, simulate pre-1.5 signature
- if ( typeof url === "object" ) {
- options = url;
- url = undefined;
- }
-
- // Force options to be an object
- options = options || {};
-
- var // Create the final options object
- s = jQuery.ajaxSetup( {}, options ),
- // Callbacks context
- callbackContext = s.context || s,
- // Context for global events
- // It's the callbackContext if one was provided in the options
- // and if it's a DOM node or a jQuery collection
- globalEventContext = callbackContext !== s &&
- ( callbackContext.nodeType || callbackContext instanceof jQuery ) ?
- jQuery( callbackContext ) : jQuery.event,
- // Deferreds
- deferred = jQuery.Deferred(),
- completeDeferred = jQuery.Callbacks( "once memory" ),
- // Status-dependent callbacks
- statusCode = s.statusCode || {},
- // ifModified key
- ifModifiedKey,
- // Headers (they are sent all at once)
- requestHeaders = {},
- requestHeadersNames = {},
- // Response headers
- responseHeadersString,
- responseHeaders,
- // transport
- transport,
- // timeout handle
- timeoutTimer,
- // Cross-domain detection vars
- parts,
- // The jqXHR state
- state = 0,
- // To know if global events are to be dispatched
- fireGlobals,
- // Loop variable
- i,
- // Fake xhr
- jqXHR = {
-
- readyState: 0,
-
- // Caches the header
- setRequestHeader: function( name, value ) {
- if ( !state ) {
- var lname = name.toLowerCase();
- name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name;
- requestHeaders[ name ] = value;
- }
- return this;
- },
-
- // Raw string
- getAllResponseHeaders: function() {
- return state === 2 ? responseHeadersString : null;
- },
-
- // Builds headers hashtable if needed
- getResponseHeader: function( key ) {
- var match;
- if ( state === 2 ) {
- if ( !responseHeaders ) {
- responseHeaders = {};
- while( ( match = rheaders.exec( responseHeadersString ) ) ) {
- responseHeaders[ match[1].toLowerCase() ] = match[ 2 ];
- }
- }
- match = responseHeaders[ key.toLowerCase() ];
- }
- return match === undefined ? null : match;
- },
-
- // Overrides response content-type header
- overrideMimeType: function( type ) {
- if ( !state ) {
- s.mimeType = type;
- }
- return this;
- },
-
- // Cancel the request
- abort: function( statusText ) {
- statusText = statusText || "abort";
- if ( transport ) {
- transport.abort( statusText );
- }
- done( 0, statusText );
- return this;
- }
- };
-
- // Callback for when everything is done
- // It is defined here because jslint complains if it is declared
- // at the end of the function (which would be more logical and readable)
- function done( status, nativeStatusText, responses, headers ) {
-
- // Called once
- if ( state === 2 ) {
- return;
- }
-
- // State is "done" now
- state = 2;
-
- // Clear timeout if it exists
- if ( timeoutTimer ) {
- clearTimeout( timeoutTimer );
- }
-
- // Dereference transport for early garbage collection
- // (no matter how long the jqXHR object will be used)
- transport = undefined;
-
- // Cache response headers
- responseHeadersString = headers || "";
-
- // Set readyState
- jqXHR.readyState = status > 0 ? 4 : 0;
-
- var isSuccess,
- success,
- error,
- statusText = nativeStatusText,
- response = responses ? ajaxHandleResponses( s, jqXHR, responses ) : undefined,
- lastModified,
- etag;
-
- // If successful, handle type chaining
- if ( status >= 200 && status < 300 || status === 304 ) {
-
- // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
- if ( s.ifModified ) {
-
- if ( ( lastModified = jqXHR.getResponseHeader( "Last-Modified" ) ) ) {
- jQuery.lastModified[ ifModifiedKey ] = lastModified;
- }
- if ( ( etag = jqXHR.getResponseHeader( "Etag" ) ) ) {
- jQuery.etag[ ifModifiedKey ] = etag;
- }
- }
-
- // If not modified
- if ( status === 304 ) {
-
- statusText = "notmodified";
- isSuccess = true;
-
- // If we have data
- } else {
-
- try {
- success = ajaxConvert( s, response );
- statusText = "success";
- isSuccess = true;
- } catch(e) {
- // We have a parsererror
- statusText = "parsererror";
- error = e;
- }
- }
- } else {
- // We extract error from statusText
- // then normalize statusText and status for non-aborts
- error = statusText;
- if ( !statusText || status ) {
- statusText = "error";
- if ( status < 0 ) {
- status = 0;
- }
- }
- }
-
- // Set data for the fake xhr object
- jqXHR.status = status;
- jqXHR.statusText = "" + ( nativeStatusText || statusText );
-
- // Success/Error
- if ( isSuccess ) {
- deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
- } else {
- deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
- }
-
- // Status-dependent callbacks
- jqXHR.statusCode( statusCode );
- statusCode = undefined;
-
- if ( fireGlobals ) {
- globalEventContext.trigger( "ajax" + ( isSuccess ? "Success" : "Error" ),
- [ jqXHR, s, isSuccess ? success : error ] );
- }
-
- // Complete
- completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
-
- if ( fireGlobals ) {
- globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
- // Handle the global AJAX counter
- if ( !( --jQuery.active ) ) {
- jQuery.event.trigger( "ajaxStop" );
- }
- }
- }
-
- // Attach deferreds
- deferred.promise( jqXHR );
- jqXHR.success = jqXHR.done;
- jqXHR.error = jqXHR.fail;
- jqXHR.complete = completeDeferred.add;
-
- // Status-dependent callbacks
- jqXHR.statusCode = function( map ) {
- if ( map ) {
- var tmp;
- if ( state < 2 ) {
- for ( tmp in map ) {
- statusCode[ tmp ] = [ statusCode[tmp], map[tmp] ];
- }
- } else {
- tmp = map[ jqXHR.status ];
- jqXHR.then( tmp, tmp );
- }
- }
- return this;
- };
-
- // Remove hash character (#7531: and string promotion)
- // Add protocol if not provided (#5866: IE7 issue with protocol-less urls)
- // We also use the url parameter if available
- s.url = ( ( url || s.url ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" );
-
- // Extract dataTypes list
- s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().split( rspacesAjax );
-
- // Determine if a cross-domain request is in order
- if ( s.crossDomain == null ) {
- parts = rurl.exec( s.url.toLowerCase() );
- s.crossDomain = !!( parts &&
- ( parts[ 1 ] != ajaxLocParts[ 1 ] || parts[ 2 ] != ajaxLocParts[ 2 ] ||
- ( parts[ 3 ] || ( parts[ 1 ] === "http:" ? 80 : 443 ) ) !=
- ( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? 80 : 443 ) ) )
- );
- }
-
- // Convert data if not already a string
- if ( s.data && s.processData && typeof s.data !== "string" ) {
- s.data = jQuery.param( s.data, s.traditional );
- }
-
- // Apply prefilters
- inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
-
- // If request was aborted inside a prefilter, stop there
- if ( state === 2 ) {
- return false;
- }
-
- // We can fire global events as of now if asked to
- fireGlobals = s.global;
-
- // Uppercase the type
- s.type = s.type.toUpperCase();
-
- // Determine if request has content
- s.hasContent = !rnoContent.test( s.type );
-
- // Watch for a new set of requests
- if ( fireGlobals && jQuery.active++ === 0 ) {
- jQuery.event.trigger( "ajaxStart" );
- }
-
- // More options handling for requests with no content
- if ( !s.hasContent ) {
-
- // If data is available, append data to url
- if ( s.data ) {
- s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.data;
- // #9682: remove data so that it's not used in an eventual retry
- delete s.data;
- }
-
- // Get ifModifiedKey before adding the anti-cache parameter
- ifModifiedKey = s.url;
-
- // Add anti-cache in url if needed
- if ( s.cache === false ) {
-
- var ts = jQuery.now(),
- // try replacing _= if it is there
- ret = s.url.replace( rts, "$1_=" + ts );
-
- // if nothing was replaced, add timestamp to the end
- s.url = ret + ( ( ret === s.url ) ? ( rquery.test( s.url ) ? "&" : "?" ) + "_=" + ts : "" );
- }
- }
-
- // Set the correct header, if data is being sent
- if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
- jqXHR.setRequestHeader( "Content-Type", s.contentType );
- }
-
- // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
- if ( s.ifModified ) {
- ifModifiedKey = ifModifiedKey || s.url;
- if ( jQuery.lastModified[ ifModifiedKey ] ) {
- jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ ifModifiedKey ] );
- }
- if ( jQuery.etag[ ifModifiedKey ] ) {
- jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ ifModifiedKey ] );
- }
- }
-
- // Set the Accepts header for the server, depending on the dataType
- jqXHR.setRequestHeader(
- "Accept",
- s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ?
- s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
- s.accepts[ "*" ]
- );
-
- // Check for headers option
- for ( i in s.headers ) {
- jqXHR.setRequestHeader( i, s.headers[ i ] );
- }
-
- // Allow custom headers/mimetypes and early abort
- if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) {
- // Abort if not done already
- jqXHR.abort();
- return false;
-
- }
-
- // Install callbacks on deferreds
- for ( i in { success: 1, error: 1, complete: 1 } ) {
- jqXHR[ i ]( s[ i ] );
- }
-
- // Get transport
- transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
-
- // If no transport, we auto-abort
- if ( !transport ) {
- done( -1, "No Transport" );
- } else {
- jqXHR.readyState = 1;
- // Send global event
- if ( fireGlobals ) {
- globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
- }
- // Timeout
- if ( s.async && s.timeout > 0 ) {
- timeoutTimer = setTimeout( function(){
- jqXHR.abort( "timeout" );
- }, s.timeout );
- }
-
- try {
- state = 1;
- transport.send( requestHeaders, done );
- } catch (e) {
- // Propagate exception as error if not done
- if ( state < 2 ) {
- done( -1, e );
- // Simply rethrow otherwise
- } else {
- throw e;
- }
- }
- }
-
- return jqXHR;
- },
-
- // Serialize an array of form elements or a set of
- // key/values into a query string
- param: function( a, traditional ) {
- var s = [],
- add = function( key, value ) {
- // If value is a function, invoke it and return its value
- value = jQuery.isFunction( value ) ? value() : value;
- s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value );
- };
-
- // Set traditional to true for jQuery <= 1.3.2 behavior.
- if ( traditional === undefined ) {
- traditional = jQuery.ajaxSettings.traditional;
- }
-
- // If an array was passed in, assume that it is an array of form elements.
- if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
- // Serialize the form elements
- jQuery.each( a, function() {
- add( this.name, this.value );
- });
-
- } else {
- // If traditional, encode the "old" way (the way 1.3.2 or older
- // did it), otherwise encode params recursively.
- for ( var prefix in a ) {
- buildParams( prefix, a[ prefix ], traditional, add );
- }
- }
-
- // Return the resulting serialization
- return s.join( "&" ).replace( r20, "+" );
- }
-});
-
-function buildParams( prefix, obj, traditional, add ) {
- if ( jQuery.isArray( obj ) ) {
- // Serialize array item.
- jQuery.each( obj, function( i, v ) {
- if ( traditional || rbracket.test( prefix ) ) {
- // Treat each array item as a scalar.
- add( prefix, v );
-
- } else {
- // If array item is non-scalar (array or object), encode its
- // numeric index to resolve deserialization ambiguity issues.
- // Note that rack (as of 1.0.0) can't currently deserialize
- // nested arrays properly, and attempting to do so may cause
- // a server error. Possible fixes are to modify rack's
- // deserialization algorithm or to provide an option or flag
- // to force array serialization to be shallow.
- buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add );
- }
- });
-
- } else if ( !traditional && jQuery.type( obj ) === "object" ) {
- // Serialize object item.
- for ( var name in obj ) {
- buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
- }
-
- } else {
- // Serialize scalar item.
- add( prefix, obj );
- }
-}
-
-// This is still on the jQuery object... for now
-// Want to move this to jQuery.ajax some day
-jQuery.extend({
-
- // Counter for holding the number of active queries
- active: 0,
-
- // Last-Modified header cache for next request
- lastModified: {},
- etag: {}
-
-});
-
-/* Handles responses to an ajax request:
- * - sets all responseXXX fields accordingly
- * - finds the right dataType (mediates between content-type and expected dataType)
- * - returns the corresponding response
- */
-function ajaxHandleResponses( s, jqXHR, responses ) {
-
- var contents = s.contents,
- dataTypes = s.dataTypes,
- responseFields = s.responseFields,
- ct,
- type,
- finalDataType,
- firstDataType;
-
- // Fill responseXXX fields
- for ( type in responseFields ) {
- if ( type in responses ) {
- jqXHR[ responseFields[type] ] = responses[ type ];
- }
- }
-
- // Remove auto dataType and get content-type in the process
- while( dataTypes[ 0 ] === "*" ) {
- dataTypes.shift();
- if ( ct === undefined ) {
- ct = s.mimeType || jqXHR.getResponseHeader( "content-type" );
- }
- }
-
- // Check if we're dealing with a known content-type
- if ( ct ) {
- for ( type in contents ) {
- if ( contents[ type ] && contents[ type ].test( ct ) ) {
- dataTypes.unshift( type );
- break;
- }
- }
- }
-
- // Check to see if we have a response for the expected dataType
- if ( dataTypes[ 0 ] in responses ) {
- finalDataType = dataTypes[ 0 ];
- } else {
- // Try convertible dataTypes
- for ( type in responses ) {
- if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) {
- finalDataType = type;
- break;
- }
- if ( !firstDataType ) {
- firstDataType = type;
- }
- }
- // Or just use first one
- finalDataType = finalDataType || firstDataType;
- }
-
- // If we found a dataType
- // We add the dataType to the list if needed
- // and return the corresponding response
- if ( finalDataType ) {
- if ( finalDataType !== dataTypes[ 0 ] ) {
- dataTypes.unshift( finalDataType );
- }
- return responses[ finalDataType ];
- }
-}
-
-// Chain conversions given the request and the original response
-function ajaxConvert( s, response ) {
-
- // Apply the dataFilter if provided
- if ( s.dataFilter ) {
- response = s.dataFilter( response, s.dataType );
- }
-
- var dataTypes = s.dataTypes,
- converters = {},
- i,
- key,
- length = dataTypes.length,
- tmp,
- // Current and previous dataTypes
- current = dataTypes[ 0 ],
- prev,
- // Conversion expression
- conversion,
- // Conversion function
- conv,
- // Conversion functions (transitive conversion)
- conv1,
- conv2;
-
- // For each dataType in the chain
- for ( i = 1; i < length; i++ ) {
-
- // Create converters map
- // with lowercased keys
- if ( i === 1 ) {
- for ( key in s.converters ) {
- if ( typeof key === "string" ) {
- converters[ key.toLowerCase() ] = s.converters[ key ];
- }
- }
- }
-
- // Get the dataTypes
- prev = current;
- current = dataTypes[ i ];
-
- // If current is auto dataType, update it to prev
- if ( current === "*" ) {
- current = prev;
- // If no auto and dataTypes are actually different
- } else if ( prev !== "*" && prev !== current ) {
-
- // Get the converter
- conversion = prev + " " + current;
- conv = converters[ conversion ] || converters[ "* " + current ];
-
- // If there is no direct converter, search transitively
- if ( !conv ) {
- conv2 = undefined;
- for ( conv1 in converters ) {
- tmp = conv1.split( " " );
- if ( tmp[ 0 ] === prev || tmp[ 0 ] === "*" ) {
- conv2 = converters[ tmp[1] + " " + current ];
- if ( conv2 ) {
- conv1 = converters[ conv1 ];
- if ( conv1 === true ) {
- conv = conv2;
- } else if ( conv2 === true ) {
- conv = conv1;
- }
- break;
- }
- }
- }
- }
- // If we found no converter, dispatch an error
- if ( !( conv || conv2 ) ) {
- jQuery.error( "No conversion from " + conversion.replace(" "," to ") );
- }
- // If found converter is not an equivalence
- if ( conv !== true ) {
- // Convert with 1 or 2 converters accordingly
- response = conv ? conv( response ) : conv2( conv1(response) );
- }
- }
- }
- return response;
-}
-
-
-
-
-var jsc = jQuery.now(),
- jsre = /(\=)\?(&|$)|\?\?/i;
-
-// Default jsonp settings
-jQuery.ajaxSetup({
- jsonp: "callback",
- jsonpCallback: function() {
- return jQuery.expando + "_" + ( jsc++ );
- }
-});
-
-// Detect, normalize options and install callbacks for jsonp requests
-jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
-
- var inspectData = ( typeof s.data === "string" ) && /^application\/x\-www\-form\-urlencoded/.test( s.contentType );
-
- if ( s.dataTypes[ 0 ] === "jsonp" ||
- s.jsonp !== false && ( jsre.test( s.url ) ||
- inspectData && jsre.test( s.data ) ) ) {
-
- var responseContainer,
- jsonpCallback = s.jsonpCallback =
- jQuery.isFunction( s.jsonpCallback ) ? s.jsonpCallback() : s.jsonpCallback,
- previous = window[ jsonpCallback ],
- url = s.url,
- data = s.data,
- replace = "$1" + jsonpCallback + "$2";
-
- if ( s.jsonp !== false ) {
- url = url.replace( jsre, replace );
- if ( s.url === url ) {
- if ( inspectData ) {
- data = data.replace( jsre, replace );
- }
- if ( s.data === data ) {
- // Add callback manually
- url += (/\?/.test( url ) ? "&" : "?") + s.jsonp + "=" + jsonpCallback;
- }
- }
- }
-
- s.url = url;
- s.data = data;
-
- // Install callback
- window[ jsonpCallback ] = function( response ) {
- responseContainer = [ response ];
- };
-
- // Clean-up function
- jqXHR.always(function() {
- // Set callback back to previous value
- window[ jsonpCallback ] = previous;
- // Call if it was a function and we have a response
- if ( responseContainer && jQuery.isFunction( previous ) ) {
- window[ jsonpCallback ]( responseContainer[ 0 ] );
- }
- });
-
- // Use data converter to retrieve json after script execution
- s.converters["script json"] = function() {
- if ( !responseContainer ) {
- jQuery.error( jsonpCallback + " was not called" );
- }
- return responseContainer[ 0 ];
- };
-
- // force json dataType
- s.dataTypes[ 0 ] = "json";
-
- // Delegate to script
- return "script";
- }
-});
-
-
-
-
-// Install script dataType
-jQuery.ajaxSetup({
- accepts: {
- script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"
- },
- contents: {
- script: /javascript|ecmascript/
- },
- converters: {
- "text script": function( text ) {
- jQuery.globalEval( text );
- return text;
- }
- }
-});
-
-// Handle cache's special case and global
-jQuery.ajaxPrefilter( "script", function( s ) {
- if ( s.cache === undefined ) {
- s.cache = false;
- }
- if ( s.crossDomain ) {
- s.type = "GET";
- s.global = false;
- }
-});
-
-// Bind script tag hack transport
-jQuery.ajaxTransport( "script", function(s) {
-
- // This transport only deals with cross domain requests
- if ( s.crossDomain ) {
-
- var script,
- head = document.head || document.getElementsByTagName( "head" )[0] || document.documentElement;
-
- return {
-
- send: function( _, callback ) {
-
- script = document.createElement( "script" );
-
- script.async = "async";
-
- if ( s.scriptCharset ) {
- script.charset = s.scriptCharset;
- }
-
- script.src = s.url;
-
- // Attach handlers for all browsers
- script.onload = script.onreadystatechange = function( _, isAbort ) {
-
- if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) {
-
- // Handle memory leak in IE
- script.onload = script.onreadystatechange = null;
-
- // Remove the script
- if ( head && script.parentNode ) {
- head.removeChild( script );
- }
-
- // Dereference the script
- script = undefined;
-
- // Callback if not abort
- if ( !isAbort ) {
- callback( 200, "success" );
- }
- }
- };
- // Use insertBefore instead of appendChild to circumvent an IE6 bug.
- // This arises when a base node is used (#2709 and #4378).
- head.insertBefore( script, head.firstChild );
- },
-
- abort: function() {
- if ( script ) {
- script.onload( 0, 1 );
- }
- }
- };
- }
-});
-
-
-
-
-var // #5280: Internet Explorer will keep connections alive if we don't abort on unload
- xhrOnUnloadAbort = window.ActiveXObject ? function() {
- // Abort all pending requests
- for ( var key in xhrCallbacks ) {
- xhrCallbacks[ key ]( 0, 1 );
- }
- } : false,
- xhrId = 0,
- xhrCallbacks;
-
-// Functions to create xhrs
-function createStandardXHR() {
- try {
- return new window.XMLHttpRequest();
- } catch( e ) {}
-}
-
-function createActiveXHR() {
- try {
- return new window.ActiveXObject( "Microsoft.XMLHTTP" );
- } catch( e ) {}
-}
-
-// Create the request object
-// (This is still attached to ajaxSettings for backward compatibility)
-jQuery.ajaxSettings.xhr = window.ActiveXObject ?
- /* Microsoft failed to properly
- * implement the XMLHttpRequest in IE7 (can't request local files),
- * so we use the ActiveXObject when it is available
- * Additionally XMLHttpRequest can be disabled in IE7/IE8 so
- * we need a fallback.
- */
- function() {
- return !this.isLocal && createStandardXHR() || createActiveXHR();
- } :
- // For all other browsers, use the standard XMLHttpRequest object
- createStandardXHR;
-
-// Determine support properties
-(function( xhr ) {
- jQuery.extend( jQuery.support, {
- ajax: !!xhr,
- cors: !!xhr && ( "withCredentials" in xhr )
- });
-})( jQuery.ajaxSettings.xhr() );
-
-// Create transport if the browser can provide an xhr
-if ( jQuery.support.ajax ) {
-
- jQuery.ajaxTransport(function( s ) {
- // Cross domain only allowed if supported through XMLHttpRequest
- if ( !s.crossDomain || jQuery.support.cors ) {
-
- var callback;
-
- return {
- send: function( headers, complete ) {
-
- // Get a new xhr
- var xhr = s.xhr(),
- handle,
- i;
-
- // Open the socket
- // Passing null username, generates a login popup on Opera (#2865)
- if ( s.username ) {
- xhr.open( s.type, s.url, s.async, s.username, s.password );
- } else {
- xhr.open( s.type, s.url, s.async );
- }
-
- // Apply custom fields if provided
- if ( s.xhrFields ) {
- for ( i in s.xhrFields ) {
- xhr[ i ] = s.xhrFields[ i ];
- }
- }
-
- // Override mime type if needed
- if ( s.mimeType && xhr.overrideMimeType ) {
- xhr.overrideMimeType( s.mimeType );
- }
-
- // X-Requested-With header
- // For cross-domain requests, seeing as conditions for a preflight are
- // akin to a jigsaw puzzle, we simply never set it to be sure.
- // (it can always be set on a per-request basis or even using ajaxSetup)
- // For same-domain requests, won't change header if already provided.
- if ( !s.crossDomain && !headers["X-Requested-With"] ) {
- headers[ "X-Requested-With" ] = "XMLHttpRequest";
- }
-
- // Need an extra try/catch for cross domain requests in Firefox 3
- try {
- for ( i in headers ) {
- xhr.setRequestHeader( i, headers[ i ] );
- }
- } catch( _ ) {}
-
- // Do send the request
- // This may raise an exception which is actually
- // handled in jQuery.ajax (so no try/catch here)
- xhr.send( ( s.hasContent && s.data ) || null );
-
- // Listener
- callback = function( _, isAbort ) {
-
- var status,
- statusText,
- responseHeaders,
- responses,
- xml;
-
- // Firefox throws exceptions when accessing properties
- // of an xhr when a network error occured
- // http://helpful.knobs-dials.com/index.php/Component_returned_failure_code:_0x80040111_(NS_ERROR_NOT_AVAILABLE)
- try {
-
- // Was never called and is aborted or complete
- if ( callback && ( isAbort || xhr.readyState === 4 ) ) {
-
- // Only called once
- callback = undefined;
-
- // Do not keep as active anymore
- if ( handle ) {
- xhr.onreadystatechange = jQuery.noop;
- if ( xhrOnUnloadAbort ) {
- delete xhrCallbacks[ handle ];
- }
- }
-
- // If it's an abort
- if ( isAbort ) {
- // Abort it manually if needed
- if ( xhr.readyState !== 4 ) {
- xhr.abort();
- }
- } else {
- status = xhr.status;
- responseHeaders = xhr.getAllResponseHeaders();
- responses = {};
- xml = xhr.responseXML;
-
- // Construct response list
- if ( xml && xml.documentElement /* #4958 */ ) {
- responses.xml = xml;
- }
-
- // When requesting binary data, IE6-9 will throw an exception
- // on any attempt to access responseText (#11426)
- try {
- responses.text = xhr.responseText;
- } catch( _ ) {
- }
-
- // Firefox throws an exception when accessing
- // statusText for faulty cross-domain requests
- try {
- statusText = xhr.statusText;
- } catch( e ) {
- // We normalize with Webkit giving an empty statusText
- statusText = "";
- }
-
- // Filter status for non standard behaviors
-
- // If the request is local and we have data: assume a success
- // (success with no data won't get notified, that's the best we
- // can do given current implementations)
- if ( !status && s.isLocal && !s.crossDomain ) {
- status = responses.text ? 200 : 404;
- // IE - #1450: sometimes returns 1223 when it should be 204
- } else if ( status === 1223 ) {
- status = 204;
- }
- }
- }
- } catch( firefoxAccessException ) {
- if ( !isAbort ) {
- complete( -1, firefoxAccessException );
- }
- }
-
- // Call complete if needed
- if ( responses ) {
- complete( status, statusText, responses, responseHeaders );
- }
- };
-
- // if we're in sync mode or it's in cache
- // and has been retrieved directly (IE6 & IE7)
- // we need to manually fire the callback
- if ( !s.async || xhr.readyState === 4 ) {
- callback();
- } else {
- handle = ++xhrId;
- if ( xhrOnUnloadAbort ) {
- // Create the active xhrs callbacks list if needed
- // and attach the unload handler
- if ( !xhrCallbacks ) {
- xhrCallbacks = {};
- jQuery( window ).unload( xhrOnUnloadAbort );
- }
- // Add to list of active xhrs callbacks
- xhrCallbacks[ handle ] = callback;
- }
- xhr.onreadystatechange = callback;
- }
- },
-
- abort: function() {
- if ( callback ) {
- callback(0,1);
- }
- }
- };
- }
- });
-}
-
-
-
-
-var elemdisplay = {},
- iframe, iframeDoc,
- rfxtypes = /^(?:toggle|show|hide)$/,
- rfxnum = /^([+\-]=)?([\d+.\-]+)([a-z%]*)$/i,
- timerId,
- fxAttrs = [
- // height animations
- [ "height", "marginTop", "marginBottom", "paddingTop", "paddingBottom" ],
- // width animations
- [ "width", "marginLeft", "marginRight", "paddingLeft", "paddingRight" ],
- // opacity animations
- [ "opacity" ]
- ],
- fxNow;
-
-jQuery.fn.extend({
- show: function( speed, easing, callback ) {
- var elem, display;
-
- if ( speed || speed === 0 ) {
- return this.animate( genFx("show", 3), speed, easing, callback );
-
- } else {
- for ( var i = 0, j = this.length; i < j; i++ ) {
- elem = this[ i ];
-
- if ( elem.style ) {
- display = elem.style.display;
-
- // Reset the inline display of this element to learn if it is
- // being hidden by cascaded rules or not
- if ( !jQuery._data(elem, "olddisplay") && display === "none" ) {
- display = elem.style.display = "";
- }
-
- // Set elements which have been overridden with display: none
- // in a stylesheet to whatever the default browser style is
- // for such an element
- if ( (display === "" && jQuery.css(elem, "display") === "none") ||
- !jQuery.contains( elem.ownerDocument.documentElement, elem ) ) {
- jQuery._data( elem, "olddisplay", defaultDisplay(elem.nodeName) );
- }
- }
- }
-
- // Set the display of most of the elements in a second loop
- // to avoid the constant reflow
- for ( i = 0; i < j; i++ ) {
- elem = this[ i ];
-
- if ( elem.style ) {
- display = elem.style.display;
-
- if ( display === "" || display === "none" ) {
- elem.style.display = jQuery._data( elem, "olddisplay" ) || "";
- }
- }
- }
-
- return this;
- }
- },
-
- hide: function( speed, easing, callback ) {
- if ( speed || speed === 0 ) {
- return this.animate( genFx("hide", 3), speed, easing, callback);
-
- } else {
- var elem, display,
- i = 0,
- j = this.length;
-
- for ( ; i < j; i++ ) {
- elem = this[i];
- if ( elem.style ) {
- display = jQuery.css( elem, "display" );
-
- if ( display !== "none" && !jQuery._data( elem, "olddisplay" ) ) {
- jQuery._data( elem, "olddisplay", display );
- }
- }
- }
-
- // Set the display of the elements in a second loop
- // to avoid the constant reflow
- for ( i = 0; i < j; i++ ) {
- if ( this[i].style ) {
- this[i].style.display = "none";
- }
- }
-
- return this;
- }
- },
-
- // Save the old toggle function
- _toggle: jQuery.fn.toggle,
-
- toggle: function( fn, fn2, callback ) {
- var bool = typeof fn === "boolean";
-
- if ( jQuery.isFunction(fn) && jQuery.isFunction(fn2) ) {
- this._toggle.apply( this, arguments );
-
- } else if ( fn == null || bool ) {
- this.each(function() {
- var state = bool ? fn : jQuery(this).is(":hidden");
- jQuery(this)[ state ? "show" : "hide" ]();
- });
-
- } else {
- this.animate(genFx("toggle", 3), fn, fn2, callback);
- }
-
- return this;
- },
-
- fadeTo: function( speed, to, easing, callback ) {
- return this.filter(":hidden").css("opacity", 0).show().end()
- .animate({opacity: to}, speed, easing, callback);
- },
-
- animate: function( prop, speed, easing, callback ) {
- var optall = jQuery.speed( speed, easing, callback );
-
- if ( jQuery.isEmptyObject( prop ) ) {
- return this.each( optall.complete, [ false ] );
- }
-
- // Do not change referenced properties as per-property easing will be lost
- prop = jQuery.extend( {}, prop );
-
- function doAnimation() {
- // XXX 'this' does not always have a nodeName when running the
- // test suite
-
- if ( optall.queue === false ) {
- jQuery._mark( this );
- }
-
- var opt = jQuery.extend( {}, optall ),
- isElement = this.nodeType === 1,
- hidden = isElement && jQuery(this).is(":hidden"),
- name, val, p, e, hooks, replace,
- parts, start, end, unit,
- method;
-
- // will store per property easing and be used to determine when an animation is complete
- opt.animatedProperties = {};
-
- // first pass over propertys to expand / normalize
- for ( p in prop ) {
- name = jQuery.camelCase( p );
- if ( p !== name ) {
- prop[ name ] = prop[ p ];
- delete prop[ p ];
- }
-
- if ( ( hooks = jQuery.cssHooks[ name ] ) && "expand" in hooks ) {
- replace = hooks.expand( prop[ name ] );
- delete prop[ name ];
-
- // not quite $.extend, this wont overwrite keys already present.
- // also - reusing 'p' from above because we have the correct "name"
- for ( p in replace ) {
- if ( ! ( p in prop ) ) {
- prop[ p ] = replace[ p ];
- }
- }
- }
- }
-
- for ( name in prop ) {
- val = prop[ name ];
- // easing resolution: per property > opt.specialEasing > opt.easing > 'swing' (default)
- if ( jQuery.isArray( val ) ) {
- opt.animatedProperties[ name ] = val[ 1 ];
- val = prop[ name ] = val[ 0 ];
- } else {
- opt.animatedProperties[ name ] = opt.specialEasing && opt.specialEasing[ name ] || opt.easing || 'swing';
- }
-
- if ( val === "hide" && hidden || val === "show" && !hidden ) {
- return opt.complete.call( this );
- }
-
- if ( isElement && ( name === "height" || name === "width" ) ) {
- // Make sure that nothing sneaks out
- // Record all 3 overflow attributes because IE does not
- // change the overflow attribute when overflowX and
- // overflowY are set to the same value
- opt.overflow = [ this.style.overflow, this.style.overflowX, this.style.overflowY ];
-
- // Set display property to inline-block for height/width
- // animations on inline elements that are having width/height animated
- if ( jQuery.css( this, "display" ) === "inline" &&
- jQuery.css( this, "float" ) === "none" ) {
-
- // inline-level elements accept inline-block;
- // block-level elements need to be inline with layout
- if ( !jQuery.support.inlineBlockNeedsLayout || defaultDisplay( this.nodeName ) === "inline" ) {
- this.style.display = "inline-block";
-
- } else {
- this.style.zoom = 1;
- }
- }
- }
- }
-
- if ( opt.overflow != null ) {
- this.style.overflow = "hidden";
- }
-
- for ( p in prop ) {
- e = new jQuery.fx( this, opt, p );
- val = prop[ p ];
-
- if ( rfxtypes.test( val ) ) {
-
- // Tracks whether to show or hide based on private
- // data attached to the element
- method = jQuery._data( this, "toggle" + p ) || ( val === "toggle" ? hidden ? "show" : "hide" : 0 );
- if ( method ) {
- jQuery._data( this, "toggle" + p, method === "show" ? "hide" : "show" );
- e[ method ]();
- } else {
- e[ val ]();
- }
-
- } else {
- parts = rfxnum.exec( val );
- start = e.cur();
-
- if ( parts ) {
- end = parseFloat( parts[2] );
- unit = parts[3] || ( jQuery.cssNumber[ p ] ? "" : "px" );
-
- // We need to compute starting value
- if ( unit !== "px" ) {
- jQuery.style( this, p, (end || 1) + unit);
- start = ( (end || 1) / e.cur() ) * start;
- jQuery.style( this, p, start + unit);
- }
-
- // If a +=/-= token was provided, we're doing a relative animation
- if ( parts[1] ) {
- end = ( (parts[ 1 ] === "-=" ? -1 : 1) * end ) + start;
- }
-
- e.custom( start, end, unit );
-
- } else {
- e.custom( start, val, "" );
- }
- }
- }
-
- // For JS strict compliance
- return true;
- }
-
- return optall.queue === false ?
- this.each( doAnimation ) :
- this.queue( optall.queue, doAnimation );
- },
-
- stop: function( type, clearQueue, gotoEnd ) {
- if ( typeof type !== "string" ) {
- gotoEnd = clearQueue;
- clearQueue = type;
- type = undefined;
- }
- if ( clearQueue && type !== false ) {
- this.queue( type || "fx", [] );
- }
-
- return this.each(function() {
- var index,
- hadTimers = false,
- timers = jQuery.timers,
- data = jQuery._data( this );
-
- // clear marker counters if we know they won't be
- if ( !gotoEnd ) {
- jQuery._unmark( true, this );
- }
-
- function stopQueue( elem, data, index ) {
- var hooks = data[ index ];
- jQuery.removeData( elem, index, true );
- hooks.stop( gotoEnd );
- }
-
- if ( type == null ) {
- for ( index in data ) {
- if ( data[ index ] && data[ index ].stop && index.indexOf(".run") === index.length - 4 ) {
- stopQueue( this, data, index );
- }
- }
- } else if ( data[ index = type + ".run" ] && data[ index ].stop ){
- stopQueue( this, data, index );
- }
-
- for ( index = timers.length; index--; ) {
- if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) {
- if ( gotoEnd ) {
-
- // force the next step to be the last
- timers[ index ]( true );
- } else {
- timers[ index ].saveState();
- }
- hadTimers = true;
- timers.splice( index, 1 );
- }
- }
-
- // start the next in the queue if the last step wasn't forced
- // timers currently will call their complete callbacks, which will dequeue
- // but only if they were gotoEnd
- if ( !( gotoEnd && hadTimers ) ) {
- jQuery.dequeue( this, type );
- }
- });
- }
-
-});
-
-// Animations created synchronously will run synchronously
-function createFxNow() {
- setTimeout( clearFxNow, 0 );
- return ( fxNow = jQuery.now() );
-}
-
-function clearFxNow() {
- fxNow = undefined;
-}
-
-// Generate parameters to create a standard animation
-function genFx( type, num ) {
- var obj = {};
-
- jQuery.each( fxAttrs.concat.apply([], fxAttrs.slice( 0, num )), function() {
- obj[ this ] = type;
- });
-
- return obj;
-}
-
-// Generate shortcuts for custom animations
-jQuery.each({
- slideDown: genFx( "show", 1 ),
- slideUp: genFx( "hide", 1 ),
- slideToggle: genFx( "toggle", 1 ),
- fadeIn: { opacity: "show" },
- fadeOut: { opacity: "hide" },
- fadeToggle: { opacity: "toggle" }
-}, function( name, props ) {
- jQuery.fn[ name ] = function( speed, easing, callback ) {
- return this.animate( props, speed, easing, callback );
- };
-});
-
-jQuery.extend({
- speed: function( speed, easing, fn ) {
- var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
- complete: fn || !fn && easing ||
- jQuery.isFunction( speed ) && speed,
- duration: speed,
- easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
- };
-
- opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration :
- opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default;
-
- // normalize opt.queue - true/undefined/null -> "fx"
- if ( opt.queue == null || opt.queue === true ) {
- opt.queue = "fx";
- }
-
- // Queueing
- opt.old = opt.complete;
-
- opt.complete = function( noUnmark ) {
- if ( jQuery.isFunction( opt.old ) ) {
- opt.old.call( this );
- }
-
- if ( opt.queue ) {
- jQuery.dequeue( this, opt.queue );
- } else if ( noUnmark !== false ) {
- jQuery._unmark( this );
- }
- };
-
- return opt;
- },
-
- easing: {
- linear: function( p ) {
- return p;
- },
- swing: function( p ) {
- return ( -Math.cos( p*Math.PI ) / 2 ) + 0.5;
- }
- },
-
- timers: [],
-
- fx: function( elem, options, prop ) {
- this.options = options;
- this.elem = elem;
- this.prop = prop;
-
- options.orig = options.orig || {};
- }
-
-});
-
-jQuery.fx.prototype = {
- // Simple function for setting a style value
- update: function() {
- if ( this.options.step ) {
- this.options.step.call( this.elem, this.now, this );
- }
-
- ( jQuery.fx.step[ this.prop ] || jQuery.fx.step._default )( this );
- },
-
- // Get the current size
- cur: function() {
- if ( this.elem[ this.prop ] != null && (!this.elem.style || this.elem.style[ this.prop ] == null) ) {
- return this.elem[ this.prop ];
- }
-
- var parsed,
- r = jQuery.css( this.elem, this.prop );
- // Empty strings, null, undefined and "auto" are converted to 0,
- // complex values such as "rotate(1rad)" are returned as is,
- // simple values such as "10px" are parsed to Float.
- return isNaN( parsed = parseFloat( r ) ) ? !r || r === "auto" ? 0 : r : parsed;
- },
-
- // Start an animation from one number to another
- custom: function( from, to, unit ) {
- var self = this,
- fx = jQuery.fx;
-
- this.startTime = fxNow || createFxNow();
- this.end = to;
- this.now = this.start = from;
- this.pos = this.state = 0;
- this.unit = unit || this.unit || ( jQuery.cssNumber[ this.prop ] ? "" : "px" );
-
- function t( gotoEnd ) {
- return self.step( gotoEnd );
- }
-
- t.queue = this.options.queue;
- t.elem = this.elem;
- t.saveState = function() {
- if ( jQuery._data( self.elem, "fxshow" + self.prop ) === undefined ) {
- if ( self.options.hide ) {
- jQuery._data( self.elem, "fxshow" + self.prop, self.start );
- } else if ( self.options.show ) {
- jQuery._data( self.elem, "fxshow" + self.prop, self.end );
- }
- }
- };
-
- if ( t() && jQuery.timers.push(t) && !timerId ) {
- timerId = setInterval( fx.tick, fx.interval );
- }
- },
-
- // Simple 'show' function
- show: function() {
- var dataShow = jQuery._data( this.elem, "fxshow" + this.prop );
-
- // Remember where we started, so that we can go back to it later
- this.options.orig[ this.prop ] = dataShow || jQuery.style( this.elem, this.prop );
- this.options.show = true;
-
- // Begin the animation
- // Make sure that we start at a small width/height to avoid any flash of content
- if ( dataShow !== undefined ) {
- // This show is picking up where a previous hide or show left off
- this.custom( this.cur(), dataShow );
- } else {
- this.custom( this.prop === "width" || this.prop === "height" ? 1 : 0, this.cur() );
- }
-
- // Start by showing the element
- jQuery( this.elem ).show();
- },
-
- // Simple 'hide' function
- hide: function() {
- // Remember where we started, so that we can go back to it later
- this.options.orig[ this.prop ] = jQuery._data( this.elem, "fxshow" + this.prop ) || jQuery.style( this.elem, this.prop );
- this.options.hide = true;
-
- // Begin the animation
- this.custom( this.cur(), 0 );
- },
-
- // Each step of an animation
- step: function( gotoEnd ) {
- var p, n, complete,
- t = fxNow || createFxNow(),
- done = true,
- elem = this.elem,
- options = this.options;
-
- if ( gotoEnd || t >= options.duration + this.startTime ) {
- this.now = this.end;
- this.pos = this.state = 1;
- this.update();
-
- options.animatedProperties[ this.prop ] = true;
-
- for ( p in options.animatedProperties ) {
- if ( options.animatedProperties[ p ] !== true ) {
- done = false;
- }
- }
-
- if ( done ) {
- // Reset the overflow
- if ( options.overflow != null && !jQuery.support.shrinkWrapBlocks ) {
-
- jQuery.each( [ "", "X", "Y" ], function( index, value ) {
- elem.style[ "overflow" + value ] = options.overflow[ index ];
- });
- }
-
- // Hide the element if the "hide" operation was done
- if ( options.hide ) {
- jQuery( elem ).hide();
- }
-
- // Reset the properties, if the item has been hidden or shown
- if ( options.hide || options.show ) {
- for ( p in options.animatedProperties ) {
- jQuery.style( elem, p, options.orig[ p ] );
- jQuery.removeData( elem, "fxshow" + p, true );
- // Toggle data is no longer needed
- jQuery.removeData( elem, "toggle" + p, true );
- }
- }
-
- // Execute the complete function
- // in the event that the complete function throws an exception
- // we must ensure it won't be called twice. #5684
-
- complete = options.complete;
- if ( complete ) {
-
- options.complete = false;
- complete.call( elem );
- }
- }
-
- return false;
-
- } else {
- // classical easing cannot be used with an Infinity duration
- if ( options.duration == Infinity ) {
- this.now = t;
- } else {
- n = t - this.startTime;
- this.state = n / options.duration;
-
- // Perform the easing function, defaults to swing
- this.pos = jQuery.easing[ options.animatedProperties[this.prop] ]( this.state, n, 0, 1, options.duration );
- this.now = this.start + ( (this.end - this.start) * this.pos );
- }
- // Perform the next step of the animation
- this.update();
- }
-
- return true;
- }
-};
-
-jQuery.extend( jQuery.fx, {
- tick: function() {
- var timer,
- timers = jQuery.timers,
- i = 0;
-
- for ( ; i < timers.length; i++ ) {
- timer = timers[ i ];
- // Checks the timer has not already been removed
- if ( !timer() && timers[ i ] === timer ) {
- timers.splice( i--, 1 );
- }
- }
-
- if ( !timers.length ) {
- jQuery.fx.stop();
- }
- },
-
- interval: 13,
-
- stop: function() {
- clearInterval( timerId );
- timerId = null;
- },
-
- speeds: {
- slow: 600,
- fast: 200,
- // Default speed
- _default: 400
- },
-
- step: {
- opacity: function( fx ) {
- jQuery.style( fx.elem, "opacity", fx.now );
- },
-
- _default: function( fx ) {
- if ( fx.elem.style && fx.elem.style[ fx.prop ] != null ) {
- fx.elem.style[ fx.prop ] = fx.now + fx.unit;
- } else {
- fx.elem[ fx.prop ] = fx.now;
- }
- }
- }
-});
-
-// Ensure props that can't be negative don't go there on undershoot easing
-jQuery.each( fxAttrs.concat.apply( [], fxAttrs ), function( i, prop ) {
- // exclude marginTop, marginLeft, marginBottom and marginRight from this list
- if ( prop.indexOf( "margin" ) ) {
- jQuery.fx.step[ prop ] = function( fx ) {
- jQuery.style( fx.elem, prop, Math.max(0, fx.now) + fx.unit );
- };
- }
-});
-
-if ( jQuery.expr && jQuery.expr.filters ) {
- jQuery.expr.filters.animated = function( elem ) {
- return jQuery.grep(jQuery.timers, function( fn ) {
- return elem === fn.elem;
- }).length;
- };
-}
-
-// Try to restore the default display value of an element
-function defaultDisplay( nodeName ) {
-
- if ( !elemdisplay[ nodeName ] ) {
-
- var body = document.body,
- elem = jQuery( "<" + nodeName + ">" ).appendTo( body ),
- display = elem.css( "display" );
- elem.remove();
-
- // If the simple way fails,
- // get element's real default display by attaching it to a temp iframe
- if ( display === "none" || display === "" ) {
- // No iframe to use yet, so create it
- if ( !iframe ) {
- iframe = document.createElement( "iframe" );
- iframe.frameBorder = iframe.width = iframe.height = 0;
- }
-
- body.appendChild( iframe );
-
- // Create a cacheable copy of the iframe document on first call.
- // IE and Opera will allow us to reuse the iframeDoc without re-writing the fake HTML
- // document to it; WebKit & Firefox won't allow reusing the iframe document.
- if ( !iframeDoc || !iframe.createElement ) {
- iframeDoc = ( iframe.contentWindow || iframe.contentDocument ).document;
- iframeDoc.write( ( jQuery.support.boxModel ? "<!doctype html>" : "" ) + "<html><body>" );
- iframeDoc.close();
- }
-
- elem = iframeDoc.createElement( nodeName );
-
- iframeDoc.body.appendChild( elem );
-
- display = jQuery.css( elem, "display" );
- body.removeChild( iframe );
- }
-
- // Store the correct default display
- elemdisplay[ nodeName ] = display;
- }
-
- return elemdisplay[ nodeName ];
-}
-
-
-
-
-var getOffset,
- rtable = /^t(?:able|d|h)$/i,
- rroot = /^(?:body|html)$/i;
-
-if ( "getBoundingClientRect" in document.documentElement ) {
- getOffset = function( elem, doc, docElem, box ) {
- try {
- box = elem.getBoundingClientRect();
- } catch(e) {}
-
- // Make sure we're not dealing with a disconnected DOM node
- if ( !box || !jQuery.contains( docElem, elem ) ) {
- return box ? { top: box.top, left: box.left } : { top: 0, left: 0 };
- }
-
- var body = doc.body,
- win = getWindow( doc ),
- clientTop = docElem.clientTop || body.clientTop || 0,
- clientLeft = docElem.clientLeft || body.clientLeft || 0,
- scrollTop = win.pageYOffset || jQuery.support.boxModel && docElem.scrollTop || body.scrollTop,
- scrollLeft = win.pageXOffset || jQuery.support.boxModel && docElem.scrollLeft || body.scrollLeft,
- top = box.top + scrollTop - clientTop,
- left = box.left + scrollLeft - clientLeft;
-
- return { top: top, left: left };
- };
-
-} else {
- getOffset = function( elem, doc, docElem ) {
- var computedStyle,
- offsetParent = elem.offsetParent,
- prevOffsetParent = elem,
- body = doc.body,
- defaultView = doc.defaultView,
- prevComputedStyle = defaultView ? defaultView.getComputedStyle( elem, null ) : elem.currentStyle,
- top = elem.offsetTop,
- left = elem.offsetLeft;
-
- while ( (elem = elem.parentNode) && elem !== body && elem !== docElem ) {
- if ( jQuery.support.fixedPosition && prevComputedStyle.position === "fixed" ) {
- break;
- }
-
- computedStyle = defaultView ? defaultView.getComputedStyle(elem, null) : elem.currentStyle;
- top -= elem.scrollTop;
- left -= elem.scrollLeft;
-
- if ( elem === offsetParent ) {
- top += elem.offsetTop;
- left += elem.offsetLeft;
-
- if ( jQuery.support.doesNotAddBorder && !(jQuery.support.doesAddBorderForTableAndCells && rtable.test(elem.nodeName)) ) {
- top += parseFloat( computedStyle.borderTopWidth ) || 0;
- left += parseFloat( computedStyle.borderLeftWidth ) || 0;
- }
-
- prevOffsetParent = offsetParent;
- offsetParent = elem.offsetParent;
- }
-
- if ( jQuery.support.subtractsBorderForOverflowNotVisible && computedStyle.overflow !== "visible" ) {
- top += parseFloat( computedStyle.borderTopWidth ) || 0;
- left += parseFloat( computedStyle.borderLeftWidth ) || 0;
- }
-
- prevComputedStyle = computedStyle;
- }
-
- if ( prevComputedStyle.position === "relative" || prevComputedStyle.position === "static" ) {
- top += body.offsetTop;
- left += body.offsetLeft;
- }
-
- if ( jQuery.support.fixedPosition && prevComputedStyle.position === "fixed" ) {
- top += Math.max( docElem.scrollTop, body.scrollTop );
- left += Math.max( docElem.scrollLeft, body.scrollLeft );
- }
-
- return { top: top, left: left };
- };
-}
-
-jQuery.fn.offset = function( options ) {
- if ( arguments.length ) {
- return options === undefined ?
- this :
- this.each(function( i ) {
- jQuery.offset.setOffset( this, options, i );
- });
- }
-
- var elem = this[0],
- doc = elem && elem.ownerDocument;
-
- if ( !doc ) {
- return null;
- }
-
- if ( elem === doc.body ) {
- return jQuery.offset.bodyOffset( elem );
- }
-
- return getOffset( elem, doc, doc.documentElement );
-};
-
-jQuery.offset = {
-
- bodyOffset: function( body ) {
- var top = body.offsetTop,
- left = body.offsetLeft;
-
- if ( jQuery.support.doesNotIncludeMarginInBodyOffset ) {
- top += parseFloat( jQuery.css(body, "marginTop") ) || 0;
- left += parseFloat( jQuery.css(body, "marginLeft") ) || 0;
- }
-
- return { top: top, left: left };
- },
-
- setOffset: function( elem, options, i ) {
- var position = jQuery.css( elem, "position" );
-
- // set position first, in-case top/left are set even on static elem
- if ( position === "static" ) {
- elem.style.position = "relative";
- }
-
- var curElem = jQuery( elem ),
- curOffset = curElem.offset(),
- curCSSTop = jQuery.css( elem, "top" ),
- curCSSLeft = jQuery.css( elem, "left" ),
- calculatePosition = ( position === "absolute" || position === "fixed" ) && jQuery.inArray("auto", [curCSSTop, curCSSLeft]) > -1,
- props = {}, curPosition = {}, curTop, curLeft;
-
- // need to be able to calculate position if either top or left is auto and position is either absolute or fixed
- if ( calculatePosition ) {
- curPosition = curElem.position();
- curTop = curPosition.top;
- curLeft = curPosition.left;
- } else {
- curTop = parseFloat( curCSSTop ) || 0;
- curLeft = parseFloat( curCSSLeft ) || 0;
- }
-
- if ( jQuery.isFunction( options ) ) {
- options = options.call( elem, i, curOffset );
- }
-
- if ( options.top != null ) {
- props.top = ( options.top - curOffset.top ) + curTop;
- }
- if ( options.left != null ) {
- props.left = ( options.left - curOffset.left ) + curLeft;
- }
-
- if ( "using" in options ) {
- options.using.call( elem, props );
- } else {
- curElem.css( props );
- }
- }
-};
-
-
-jQuery.fn.extend({
-
- position: function() {
- if ( !this[0] ) {
- return null;
- }
-
- var elem = this[0],
-
- // Get *real* offsetParent
- offsetParent = this.offsetParent(),
-
- // Get correct offsets
- offset = this.offset(),
- parentOffset = rroot.test(offsetParent[0].nodeName) ? { top: 0, left: 0 } : offsetParent.offset();
-
- // Subtract element margins
- // note: when an element has margin: auto the offsetLeft and marginLeft
- // are the same in Safari causing offset.left to incorrectly be 0
- offset.top -= parseFloat( jQuery.css(elem, "marginTop") ) || 0;
- offset.left -= parseFloat( jQuery.css(elem, "marginLeft") ) || 0;
-
- // Add offsetParent borders
- parentOffset.top += parseFloat( jQuery.css(offsetParent[0], "borderTopWidth") ) || 0;
- parentOffset.left += parseFloat( jQuery.css(offsetParent[0], "borderLeftWidth") ) || 0;
-
- // Subtract the two offsets
- return {
- top: offset.top - parentOffset.top,
- left: offset.left - parentOffset.left
- };
- },
-
- offsetParent: function() {
- return this.map(function() {
- var offsetParent = this.offsetParent || document.body;
- while ( offsetParent && (!rroot.test(offsetParent.nodeName) && jQuery.css(offsetParent, "position") === "static") ) {
- offsetParent = offsetParent.offsetParent;
- }
- return offsetParent;
- });
- }
-});
-
-
-// Create scrollLeft and scrollTop methods
-jQuery.each( {scrollLeft: "pageXOffset", scrollTop: "pageYOffset"}, function( method, prop ) {
- var top = /Y/.test( prop );
-
- jQuery.fn[ method ] = function( val ) {
- return jQuery.access( this, function( elem, method, val ) {
- var win = getWindow( elem );
-
- if ( val === undefined ) {
- return win ? (prop in win) ? win[ prop ] :
- jQuery.support.boxModel && win.document.documentElement[ method ] ||
- win.document.body[ method ] :
- elem[ method ];
- }
-
- if ( win ) {
- win.scrollTo(
- !top ? val : jQuery( win ).scrollLeft(),
- top ? val : jQuery( win ).scrollTop()
- );
-
- } else {
- elem[ method ] = val;
- }
- }, method, val, arguments.length, null );
- };
-});
-
-function getWindow( elem ) {
- return jQuery.isWindow( elem ) ?
- elem :
- elem.nodeType === 9 ?
- elem.defaultView || elem.parentWindow :
- false;
-}
-
-
-
-
-// Create width, height, innerHeight, innerWidth, outerHeight and outerWidth methods
-jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
- var clientProp = "client" + name,
- scrollProp = "scroll" + name,
- offsetProp = "offset" + name;
-
- // innerHeight and innerWidth
- jQuery.fn[ "inner" + name ] = function() {
- var elem = this[0];
- return elem ?
- elem.style ?
- parseFloat( jQuery.css( elem, type, "padding" ) ) :
- this[ type ]() :
- null;
- };
-
- // outerHeight and outerWidth
- jQuery.fn[ "outer" + name ] = function( margin ) {
- var elem = this[0];
- return elem ?
- elem.style ?
- parseFloat( jQuery.css( elem, type, margin ? "margin" : "border" ) ) :
- this[ type ]() :
- null;
- };
-
- jQuery.fn[ type ] = function( value ) {
- return jQuery.access( this, function( elem, type, value ) {
- var doc, docElemProp, orig, ret;
-
- if ( jQuery.isWindow( elem ) ) {
- // 3rd condition allows Nokia support, as it supports the docElem prop but not CSS1Compat
- doc = elem.document;
- docElemProp = doc.documentElement[ clientProp ];
- return jQuery.support.boxModel && docElemProp ||
- doc.body && doc.body[ clientProp ] || docElemProp;
- }
-
- // Get document width or height
- if ( elem.nodeType === 9 ) {
- // Either scroll[Width/Height] or offset[Width/Height], whichever is greater
- doc = elem.documentElement;
-
- // when a window > document, IE6 reports a offset[Width/Height] > client[Width/Height]
- // so we can't use max, as it'll choose the incorrect offset[Width/Height]
- // instead we use the correct client[Width/Height]
- // support:IE6
- if ( doc[ clientProp ] >= doc[ scrollProp ] ) {
- return doc[ clientProp ];
- }
-
- return Math.max(
- elem.body[ scrollProp ], doc[ scrollProp ],
- elem.body[ offsetProp ], doc[ offsetProp ]
- );
- }
-
- // Get width or height on the element
- if ( value === undefined ) {
- orig = jQuery.css( elem, type );
- ret = parseFloat( orig );
- return jQuery.isNumeric( ret ) ? ret : orig;
- }
-
- // Set the width or height on the element
- jQuery( elem ).css( type, value );
- }, type, value, arguments.length, null );
- };
-});
-
-
-
-
-// Expose jQuery to the global object
-window.jQuery = window.$ = jQuery;
-
-// Expose jQuery as an AMD module, but only for AMD loaders that
-// understand the issues with loading multiple versions of jQuery
-// in a page that all might call define(). The loader will indicate
-// they have special allowances for multiple jQuery versions by
-// specifying define.amd.jQuery = true. Register as a named module,
-// since jQuery can be concatenated with other files that may use define,
-// but not use a proper concatenation script that understands anonymous
-// AMD modules. A named AMD is safest and most robust way to register.
-// Lowercase jquery is used because AMD module names are derived from
-// file names, and jQuery is normally delivered in a lowercase file name.
-// Do this after creating the global so that if an AMD module wants to call
-// noConflict to hide this version of jQuery, it will work.
-if ( typeof define === "function" && define.amd && define.amd.jQuery ) {
- define( "jquery", [], function () { return jQuery; } );
-}
-
-
-
-})( window );
diff --git a/moose-core/Docs/user/html/pymoose/_static/minus.png b/moose-core/Docs/user/html/pymoose/_static/minus.png
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diff --git a/moose-core/Docs/user/html/pymoose/_static/plus.png b/moose-core/Docs/user/html/pymoose/_static/plus.png
deleted file mode 100644
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Binary files a/moose-core/Docs/user/html/pymoose/_static/plus.png and /dev/null differ
diff --git a/moose-core/Docs/user/html/pymoose/_static/pygments.css b/moose-core/Docs/user/html/pymoose/_static/pygments.css
deleted file mode 100644
index d79caa151c28f0b24a636319b0d9d732f6c597b5..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/html/pymoose/_static/pygments.css
+++ /dev/null
@@ -1,62 +0,0 @@
-.highlight .hll { background-color: #ffffcc }
-.highlight { background: #eeffcc; }
-.highlight .c { color: #408090; font-style: italic } /* Comment */
-.highlight .err { border: 1px solid #FF0000 } /* Error */
-.highlight .k { color: #007020; font-weight: bold } /* Keyword */
-.highlight .o { color: #666666 } /* Operator */
-.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
-.highlight .cp { color: #007020 } /* Comment.Preproc */
-.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
-.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
-.highlight .gd { color: #A00000 } /* Generic.Deleted */
-.highlight .ge { font-style: italic } /* Generic.Emph */
-.highlight .gr { color: #FF0000 } /* Generic.Error */
-.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
-.highlight .gi { color: #00A000 } /* Generic.Inserted */
-.highlight .go { color: #333333 } /* Generic.Output */
-.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
-.highlight .gs { font-weight: bold } /* Generic.Strong */
-.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
-.highlight .gt { color: #0044DD } /* Generic.Traceback */
-.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
-.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
-.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
-.highlight .kp { color: #007020 } /* Keyword.Pseudo */
-.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
-.highlight .kt { color: #902000 } /* Keyword.Type */
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-.highlight .na { color: #4070a0 } /* Name.Attribute */
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-.highlight .nv { color: #bb60d5 } /* Name.Variable */
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-.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
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diff --git a/moose-core/Docs/user/html/pymoose/_static/searchtools.js b/moose-core/Docs/user/html/pymoose/_static/searchtools.js
deleted file mode 100644
index 11b85cb80f1746648236af21c9ddb6f270e0520a..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/html/pymoose/_static/searchtools.js
+++ /dev/null
@@ -1,567 +0,0 @@
-/*
- * searchtools.js_t
- * ~~~~~~~~~~~~~~~~
- *
- * Sphinx JavaScript utilties for the full-text search.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-/**
- * helper function to return a node containing the
- * search summary for a given text. keywords is a list
- * of stemmed words, hlwords is the list of normal, unstemmed
- * words. the first one is used to find the occurance, the
- * latter for highlighting it.
- */
-
-jQuery.makeSearchSummary = function(text, keywords, hlwords) {
- var textLower = text.toLowerCase();
- var start = 0;
- $.each(keywords, function() {
- var i = textLower.indexOf(this.toLowerCase());
- if (i > -1)
- start = i;
- });
- start = Math.max(start - 120, 0);
- var excerpt = ((start > 0) ? '...' : '') +
- $.trim(text.substr(start, 240)) +
- ((start + 240 - text.length) ? '...' : '');
- var rv = $('<div class="context"></div>').text(excerpt);
- $.each(hlwords, function() {
- rv = rv.highlightText(this, 'highlighted');
- });
- return rv;
-}
-
-
-/**
- * Porter Stemmer
- */
-var Stemmer = function() {
-
- var step2list = {
- ational: 'ate',
- tional: 'tion',
- enci: 'ence',
- anci: 'ance',
- izer: 'ize',
- bli: 'ble',
- alli: 'al',
- entli: 'ent',
- eli: 'e',
- ousli: 'ous',
- ization: 'ize',
- ation: 'ate',
- ator: 'ate',
- alism: 'al',
- iveness: 'ive',
- fulness: 'ful',
- ousness: 'ous',
- aliti: 'al',
- iviti: 'ive',
- biliti: 'ble',
- logi: 'log'
- };
-
- var step3list = {
- icate: 'ic',
- ative: '',
- alize: 'al',
- iciti: 'ic',
- ical: 'ic',
- ful: '',
- ness: ''
- };
-
- var c = "[^aeiou]"; // consonant
- var v = "[aeiouy]"; // vowel
- var C = c + "[^aeiouy]*"; // consonant sequence
- var V = v + "[aeiou]*"; // vowel sequence
-
- var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
- var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
- var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
- var s_v = "^(" + C + ")?" + v; // vowel in stem
-
- this.stemWord = function (w) {
- var stem;
- var suffix;
- var firstch;
- var origword = w;
-
- if (w.length < 3)
- return w;
-
- var re;
- var re2;
- var re3;
- var re4;
-
- firstch = w.substr(0,1);
- if (firstch == "y")
- w = firstch.toUpperCase() + w.substr(1);
-
- // Step 1a
- re = /^(.+?)(ss|i)es$/;
- re2 = /^(.+?)([^s])s$/;
-
- if (re.test(w))
- w = w.replace(re,"$1$2");
- else if (re2.test(w))
- w = w.replace(re2,"$1$2");
-
- // Step 1b
- re = /^(.+?)eed$/;
- re2 = /^(.+?)(ed|ing)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- re = new RegExp(mgr0);
- if (re.test(fp[1])) {
- re = /.$/;
- w = w.replace(re,"");
- }
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1];
- re2 = new RegExp(s_v);
- if (re2.test(stem)) {
- w = stem;
- re2 = /(at|bl|iz)$/;
- re3 = new RegExp("([^aeiouylsz])\\1$");
- re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re2.test(w))
- w = w + "e";
- else if (re3.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
- else if (re4.test(w))
- w = w + "e";
- }
- }
-
- // Step 1c
- re = /^(.+?)y$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(s_v);
- if (re.test(stem))
- w = stem + "i";
- }
-
- // Step 2
- re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step2list[suffix];
- }
-
- // Step 3
- re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step3list[suffix];
- }
-
- // Step 4
- re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
- re2 = /^(.+?)(s|t)(ion)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- if (re.test(stem))
- w = stem;
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1] + fp[2];
- re2 = new RegExp(mgr1);
- if (re2.test(stem))
- w = stem;
- }
-
- // Step 5
- re = /^(.+?)e$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- re2 = new RegExp(meq1);
- re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
- w = stem;
- }
- re = /ll$/;
- re2 = new RegExp(mgr1);
- if (re.test(w) && re2.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
-
- // and turn initial Y back to y
- if (firstch == "y")
- w = firstch.toLowerCase() + w.substr(1);
- return w;
- }
-}
-
-
-/**
- * Search Module
- */
-var Search = {
-
- _index : null,
- _queued_query : null,
- _pulse_status : -1,
-
- init : function() {
- var params = $.getQueryParameters();
- if (params.q) {
- var query = params.q[0];
- $('input[name="q"]')[0].value = query;
- this.performSearch(query);
- }
- },
-
- loadIndex : function(url) {
- $.ajax({type: "GET", url: url, data: null,
- dataType: "script", cache: true,
- complete: function(jqxhr, textstatus) {
- if (textstatus != "success") {
- document.getElementById("searchindexloader").src = url;
- }
- }});
- },
-
- setIndex : function(index) {
- var q;
- this._index = index;
- if ((q = this._queued_query) !== null) {
- this._queued_query = null;
- Search.query(q);
- }
- },
-
- hasIndex : function() {
- return this._index !== null;
- },
-
- deferQuery : function(query) {
- this._queued_query = query;
- },
-
- stopPulse : function() {
- this._pulse_status = 0;
- },
-
- startPulse : function() {
- if (this._pulse_status >= 0)
- return;
- function pulse() {
- Search._pulse_status = (Search._pulse_status + 1) % 4;
- var dotString = '';
- for (var i = 0; i < Search._pulse_status; i++)
- dotString += '.';
- Search.dots.text(dotString);
- if (Search._pulse_status > -1)
- window.setTimeout(pulse, 500);
- };
- pulse();
- },
-
- /**
- * perform a search for something
- */
- performSearch : function(query) {
- // create the required interface elements
- this.out = $('#search-results');
- this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
- this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p style="display: none"></p>').appendTo(this.out);
- this.output = $('<ul class="search"/>').appendTo(this.out);
-
- $('#search-progress').text(_('Preparing search...'));
- this.startPulse();
-
- // index already loaded, the browser was quick!
- if (this.hasIndex())
- this.query(query);
- else
- this.deferQuery(query);
- },
-
- query : function(query) {
- var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
-
- // Stem the searchterms and add them to the correct list
- var stemmer = new Stemmer();
- var searchterms = [];
- var excluded = [];
- var hlterms = [];
- var tmp = query.split(/\s+/);
- var objectterms = [];
- for (var i = 0; i < tmp.length; i++) {
- if (tmp[i] != "") {
- objectterms.push(tmp[i].toLowerCase());
- }
-
- if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
- tmp[i] == "") {
- // skip this "word"
- continue;
- }
- // stem the word
- var word = stemmer.stemWord(tmp[i]).toLowerCase();
- // select the correct list
- if (word[0] == '-') {
- var toAppend = excluded;
- word = word.substr(1);
- }
- else {
- var toAppend = searchterms;
- hlterms.push(tmp[i].toLowerCase());
- }
- // only add if not already in the list
- if (!$.contains(toAppend, word))
- toAppend.push(word);
- };
- var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
- // console.debug('SEARCH: searching for:');
- // console.info('required: ', searchterms);
- // console.info('excluded: ', excluded);
-
- // prepare search
- var filenames = this._index.filenames;
- var titles = this._index.titles;
- var terms = this._index.terms;
- var fileMap = {};
- var files = null;
- // different result priorities
- var importantResults = [];
- var objectResults = [];
- var regularResults = [];
- var unimportantResults = [];
- $('#search-progress').empty();
-
- // lookup as object
- for (var i = 0; i < objectterms.length; i++) {
- var others = [].concat(objectterms.slice(0,i),
- objectterms.slice(i+1, objectterms.length))
- var results = this.performObjectSearch(objectterms[i], others);
- // Assume first word is most likely to be the object,
- // other words more likely to be in description.
- // Therefore put matches for earlier words first.
- // (Results are eventually used in reverse order).
- objectResults = results[0].concat(objectResults);
- importantResults = results[1].concat(importantResults);
- unimportantResults = results[2].concat(unimportantResults);
- }
-
- // perform the search on the required terms
- for (var i = 0; i < searchterms.length; i++) {
- var word = searchterms[i];
- // no match but word was a required one
- if ((files = terms[word]) == null)
- break;
- if (files.length == undefined) {
- files = [files];
- }
- // create the mapping
- for (var j = 0; j < files.length; j++) {
- var file = files[j];
- if (file in fileMap)
- fileMap[file].push(word);
- else
- fileMap[file] = [word];
- }
- }
-
- // now check if the files don't contain excluded terms
- for (var file in fileMap) {
- var valid = true;
-
- // check if all requirements are matched
- if (fileMap[file].length != searchterms.length)
- continue;
-
- // ensure that none of the excluded terms is in the
- // search result.
- for (var i = 0; i < excluded.length; i++) {
- if (terms[excluded[i]] == file ||
- $.contains(terms[excluded[i]] || [], file)) {
- valid = false;
- break;
- }
- }
-
- // if we have still a valid result we can add it
- // to the result list
- if (valid)
- regularResults.push([filenames[file], titles[file], '', null]);
- }
-
- // delete unused variables in order to not waste
- // memory until list is retrieved completely
- delete filenames, titles, terms;
-
- // now sort the regular results descending by title
- regularResults.sort(function(a, b) {
- var left = a[1].toLowerCase();
- var right = b[1].toLowerCase();
- return (left > right) ? -1 : ((left < right) ? 1 : 0);
- });
-
- // combine all results
- var results = unimportantResults.concat(regularResults)
- .concat(objectResults).concat(importantResults);
-
- // print the results
- var resultCount = results.length;
- function displayNextItem() {
- // results left, load the summary and display it
- if (results.length) {
- var item = results.pop();
- var listItem = $('<li style="display:none"></li>');
- if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
- // dirhtml builder
- var dirname = item[0] + '/';
- if (dirname.match(/\/index\/$/)) {
- dirname = dirname.substring(0, dirname.length-6);
- } else if (dirname == 'index/') {
- dirname = '';
- }
- listItem.append($('<a/>').attr('href',
- DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
- highlightstring + item[2]).html(item[1]));
- } else {
- // normal html builders
- listItem.append($('<a/>').attr('href',
- item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
- highlightstring + item[2]).html(item[1]));
- }
- if (item[3]) {
- listItem.append($('<span> (' + item[3] + ')</span>'));
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
- dataType: "text",
- complete: function(jqxhr, textstatus) {
- var data = jqxhr.responseText;
- if (data !== '') {
- listItem.append($.makeSearchSummary(data, searchterms, hlterms));
- }
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }});
- } else {
- // no source available, just display title
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }
- }
- // search finished, update title and status message
- else {
- Search.stopPulse();
- Search.title.text(_('Search Results'));
- if (!resultCount)
- Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
- else
- Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
- Search.status.fadeIn(500);
- }
- }
- displayNextItem();
- },
-
- performObjectSearch : function(object, otherterms) {
- var filenames = this._index.filenames;
- var objects = this._index.objects;
- var objnames = this._index.objnames;
- var titles = this._index.titles;
-
- var importantResults = [];
- var objectResults = [];
- var unimportantResults = [];
-
- for (var prefix in objects) {
- for (var name in objects[prefix]) {
- var fullname = (prefix ? prefix + '.' : '') + name;
- if (fullname.toLowerCase().indexOf(object) > -1) {
- var match = objects[prefix][name];
- var objname = objnames[match[1]][2];
- var title = titles[match[0]];
- // If more than one term searched for, we require other words to be
- // found in the name/title/description
- if (otherterms.length > 0) {
- var haystack = (prefix + ' ' + name + ' ' +
- objname + ' ' + title).toLowerCase();
- var allfound = true;
- for (var i = 0; i < otherterms.length; i++) {
- if (haystack.indexOf(otherterms[i]) == -1) {
- allfound = false;
- break;
- }
- }
- if (!allfound) {
- continue;
- }
- }
- var descr = objname + _(', in ') + title;
- anchor = match[3];
- if (anchor == '')
- anchor = fullname;
- else if (anchor == '-')
- anchor = objnames[match[1]][1] + '-' + fullname;
- result = [filenames[match[0]], fullname, '#'+anchor, descr];
- switch (match[2]) {
- case 1: objectResults.push(result); break;
- case 0: importantResults.push(result); break;
- case 2: unimportantResults.push(result); break;
- }
- }
- }
- }
-
- // sort results descending
- objectResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- importantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- unimportantResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
- return [importantResults, objectResults, unimportantResults]
- }
-}
-
-$(document).ready(function() {
- Search.init();
-});
\ No newline at end of file
diff --git a/moose-core/Docs/user/html/pymoose/_static/sidebar.js b/moose-core/Docs/user/html/pymoose/_static/sidebar.js
deleted file mode 100644
index a45e1926addf0b96c1cf0180287763bbece82960..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/html/pymoose/_static/sidebar.js
+++ /dev/null
@@ -1,151 +0,0 @@
-/*
- * sidebar.js
- * ~~~~~~~~~~
- *
- * This script makes the Sphinx sidebar collapsible.
- *
- * .sphinxsidebar contains .sphinxsidebarwrapper. This script adds
- * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton
- * used to collapse and expand the sidebar.
- *
- * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden
- * and the width of the sidebar and the margin-left of the document
- * are decreased. When the sidebar is expanded the opposite happens.
- * This script saves a per-browser/per-session cookie used to
- * remember the position of the sidebar among the pages.
- * Once the browser is closed the cookie is deleted and the position
- * reset to the default (expanded).
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-$(function() {
- // global elements used by the functions.
- // the 'sidebarbutton' element is defined as global after its
- // creation, in the add_sidebar_button function
- var bodywrapper = $('.bodywrapper');
- var sidebar = $('.sphinxsidebar');
- var sidebarwrapper = $('.sphinxsidebarwrapper');
-
- // for some reason, the document has no sidebar; do not run into errors
- if (!sidebar.length) return;
-
- // original margin-left of the bodywrapper and width of the sidebar
- // with the sidebar expanded
- var bw_margin_expanded = bodywrapper.css('margin-left');
- var ssb_width_expanded = sidebar.width();
-
- // margin-left of the bodywrapper and width of the sidebar
- // with the sidebar collapsed
- var bw_margin_collapsed = '.8em';
- var ssb_width_collapsed = '.8em';
-
- // colors used by the current theme
- var dark_color = $('.related').css('background-color');
- var light_color = $('.document').css('background-color');
-
- function sidebar_is_collapsed() {
- return sidebarwrapper.is(':not(:visible)');
- }
-
- function toggle_sidebar() {
- if (sidebar_is_collapsed())
- expand_sidebar();
- else
- collapse_sidebar();
- }
-
- function collapse_sidebar() {
- sidebarwrapper.hide();
- sidebar.css('width', ssb_width_collapsed);
- bodywrapper.css('margin-left', bw_margin_collapsed);
- sidebarbutton.css({
- 'margin-left': '0',
- 'height': bodywrapper.height()
- });
- sidebarbutton.find('span').text('»');
- sidebarbutton.attr('title', _('Expand sidebar'));
- document.cookie = 'sidebar=collapsed';
- }
-
- function expand_sidebar() {
- bodywrapper.css('margin-left', bw_margin_expanded);
- sidebar.css('width', ssb_width_expanded);
- sidebarwrapper.show();
- sidebarbutton.css({
- 'margin-left': ssb_width_expanded-12,
- 'height': bodywrapper.height()
- });
- sidebarbutton.find('span').text('«');
- sidebarbutton.attr('title', _('Collapse sidebar'));
- document.cookie = 'sidebar=expanded';
- }
-
- function add_sidebar_button() {
- sidebarwrapper.css({
- 'float': 'left',
- 'margin-right': '0',
- 'width': ssb_width_expanded - 28
- });
- // create the button
- sidebar.append(
- '<div id="sidebarbutton"><span>«</span></div>'
- );
- var sidebarbutton = $('#sidebarbutton');
- light_color = sidebarbutton.css('background-color');
- // find the height of the viewport to center the '<<' in the page
- var viewport_height;
- if (window.innerHeight)
- viewport_height = window.innerHeight;
- else
- viewport_height = $(window).height();
- sidebarbutton.find('span').css({
- 'display': 'block',
- 'margin-top': (viewport_height - sidebar.position().top - 20) / 2
- });
-
- sidebarbutton.click(toggle_sidebar);
- sidebarbutton.attr('title', _('Collapse sidebar'));
- sidebarbutton.css({
- 'color': '#FFFFFF',
- 'border-left': '1px solid ' + dark_color,
- 'font-size': '1.2em',
- 'cursor': 'pointer',
- 'height': bodywrapper.height(),
- 'padding-top': '1px',
- 'margin-left': ssb_width_expanded - 12
- });
-
- sidebarbutton.hover(
- function () {
- $(this).css('background-color', dark_color);
- },
- function () {
- $(this).css('background-color', light_color);
- }
- );
- }
-
- function set_position_from_cookie() {
- if (!document.cookie)
- return;
- var items = document.cookie.split(';');
- for(var k=0; k<items.length; k++) {
- var key_val = items[k].split('=');
- var key = key_val[0];
- if (key == 'sidebar') {
- var value = key_val[1];
- if ((value == 'collapsed') && (!sidebar_is_collapsed()))
- collapse_sidebar();
- else if ((value == 'expanded') && (sidebar_is_collapsed()))
- expand_sidebar();
- }
- }
- }
-
- add_sidebar_button();
- var sidebarbutton = $('#sidebarbutton');
- set_position_from_cookie();
-});
diff --git a/moose-core/Docs/user/html/pymoose/_static/underscore.js b/moose-core/Docs/user/html/pymoose/_static/underscore.js
deleted file mode 100644
index a12f0d96cfb48a02d518427b26c333bac622810a..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/html/pymoose/_static/underscore.js
+++ /dev/null
@@ -1,1226 +0,0 @@
-// Underscore.js 1.4.4
-// http://underscorejs.org
-// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore may be freely distributed under the MIT license.
-
-(function() {
-
- // Baseline setup
- // --------------
-
- // Establish the root object, `window` in the browser, or `global` on the server.
- var root = this;
-
- // Save the previous value of the `_` variable.
- var previousUnderscore = root._;
-
- // Establish the object that gets returned to break out of a loop iteration.
- var breaker = {};
-
- // Save bytes in the minified (but not gzipped) version:
- var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
-
- // Create quick reference variables for speed access to core prototypes.
- var push = ArrayProto.push,
- slice = ArrayProto.slice,
- concat = ArrayProto.concat,
- toString = ObjProto.toString,
- hasOwnProperty = ObjProto.hasOwnProperty;
-
- // All **ECMAScript 5** native function implementations that we hope to use
- // are declared here.
- var
- nativeForEach = ArrayProto.forEach,
- nativeMap = ArrayProto.map,
- nativeReduce = ArrayProto.reduce,
- nativeReduceRight = ArrayProto.reduceRight,
- nativeFilter = ArrayProto.filter,
- nativeEvery = ArrayProto.every,
- nativeSome = ArrayProto.some,
- nativeIndexOf = ArrayProto.indexOf,
- nativeLastIndexOf = ArrayProto.lastIndexOf,
- nativeIsArray = Array.isArray,
- nativeKeys = Object.keys,
- nativeBind = FuncProto.bind;
-
- // Create a safe reference to the Underscore object for use below.
- var _ = function(obj) {
- if (obj instanceof _) return obj;
- if (!(this instanceof _)) return new _(obj);
- this._wrapped = obj;
- };
-
- // Export the Underscore object for **Node.js**, with
- // backwards-compatibility for the old `require()` API. If we're in
- // the browser, add `_` as a global object via a string identifier,
- // for Closure Compiler "advanced" mode.
- if (typeof exports !== 'undefined') {
- if (typeof module !== 'undefined' && module.exports) {
- exports = module.exports = _;
- }
- exports._ = _;
- } else {
- root._ = _;
- }
-
- // Current version.
- _.VERSION = '1.4.4';
-
- // Collection Functions
- // --------------------
-
- // The cornerstone, an `each` implementation, aka `forEach`.
- // Handles objects with the built-in `forEach`, arrays, and raw objects.
- // Delegates to **ECMAScript 5**'s native `forEach` if available.
- var each = _.each = _.forEach = function(obj, iterator, context) {
- if (obj == null) return;
- if (nativeForEach && obj.forEach === nativeForEach) {
- obj.forEach(iterator, context);
- } else if (obj.length === +obj.length) {
- for (var i = 0, l = obj.length; i < l; i++) {
- if (iterator.call(context, obj[i], i, obj) === breaker) return;
- }
- } else {
- for (var key in obj) {
- if (_.has(obj, key)) {
- if (iterator.call(context, obj[key], key, obj) === breaker) return;
- }
- }
- }
- };
-
- // Return the results of applying the iterator to each element.
- // Delegates to **ECMAScript 5**'s native `map` if available.
- _.map = _.collect = function(obj, iterator, context) {
- var results = [];
- if (obj == null) return results;
- if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
- each(obj, function(value, index, list) {
- results[results.length] = iterator.call(context, value, index, list);
- });
- return results;
- };
-
- var reduceError = 'Reduce of empty array with no initial value';
-
- // **Reduce** builds up a single result from a list of values, aka `inject`,
- // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
- _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
- var initial = arguments.length > 2;
- if (obj == null) obj = [];
- if (nativeReduce && obj.reduce === nativeReduce) {
- if (context) iterator = _.bind(iterator, context);
- return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
- }
- each(obj, function(value, index, list) {
- if (!initial) {
- memo = value;
- initial = true;
- } else {
- memo = iterator.call(context, memo, value, index, list);
- }
- });
- if (!initial) throw new TypeError(reduceError);
- return memo;
- };
-
- // The right-associative version of reduce, also known as `foldr`.
- // Delegates to **ECMAScript 5**'s native `reduceRight` if available.
- _.reduceRight = _.foldr = function(obj, iterator, memo, context) {
- var initial = arguments.length > 2;
- if (obj == null) obj = [];
- if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
- if (context) iterator = _.bind(iterator, context);
- return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
- }
- var length = obj.length;
- if (length !== +length) {
- var keys = _.keys(obj);
- length = keys.length;
- }
- each(obj, function(value, index, list) {
- index = keys ? keys[--length] : --length;
- if (!initial) {
- memo = obj[index];
- initial = true;
- } else {
- memo = iterator.call(context, memo, obj[index], index, list);
- }
- });
- if (!initial) throw new TypeError(reduceError);
- return memo;
- };
-
- // Return the first value which passes a truth test. Aliased as `detect`.
- _.find = _.detect = function(obj, iterator, context) {
- var result;
- any(obj, function(value, index, list) {
- if (iterator.call(context, value, index, list)) {
- result = value;
- return true;
- }
- });
- return result;
- };
-
- // Return all the elements that pass a truth test.
- // Delegates to **ECMAScript 5**'s native `filter` if available.
- // Aliased as `select`.
- _.filter = _.select = function(obj, iterator, context) {
- var results = [];
- if (obj == null) return results;
- if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
- each(obj, function(value, index, list) {
- if (iterator.call(context, value, index, list)) results[results.length] = value;
- });
- return results;
- };
-
- // Return all the elements for which a truth test fails.
- _.reject = function(obj, iterator, context) {
- return _.filter(obj, function(value, index, list) {
- return !iterator.call(context, value, index, list);
- }, context);
- };
-
- // Determine whether all of the elements match a truth test.
- // Delegates to **ECMAScript 5**'s native `every` if available.
- // Aliased as `all`.
- _.every = _.all = function(obj, iterator, context) {
- iterator || (iterator = _.identity);
- var result = true;
- if (obj == null) return result;
- if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
- each(obj, function(value, index, list) {
- if (!(result = result && iterator.call(context, value, index, list))) return breaker;
- });
- return !!result;
- };
-
- // Determine if at least one element in the object matches a truth test.
- // Delegates to **ECMAScript 5**'s native `some` if available.
- // Aliased as `any`.
- var any = _.some = _.any = function(obj, iterator, context) {
- iterator || (iterator = _.identity);
- var result = false;
- if (obj == null) return result;
- if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
- each(obj, function(value, index, list) {
- if (result || (result = iterator.call(context, value, index, list))) return breaker;
- });
- return !!result;
- };
-
- // Determine if the array or object contains a given value (using `===`).
- // Aliased as `include`.
- _.contains = _.include = function(obj, target) {
- if (obj == null) return false;
- if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
- return any(obj, function(value) {
- return value === target;
- });
- };
-
- // Invoke a method (with arguments) on every item in a collection.
- _.invoke = function(obj, method) {
- var args = slice.call(arguments, 2);
- var isFunc = _.isFunction(method);
- return _.map(obj, function(value) {
- return (isFunc ? method : value[method]).apply(value, args);
- });
- };
-
- // Convenience version of a common use case of `map`: fetching a property.
- _.pluck = function(obj, key) {
- return _.map(obj, function(value){ return value[key]; });
- };
-
- // Convenience version of a common use case of `filter`: selecting only objects
- // containing specific `key:value` pairs.
- _.where = function(obj, attrs, first) {
- if (_.isEmpty(attrs)) return first ? null : [];
- return _[first ? 'find' : 'filter'](obj, function(value) {
- for (var key in attrs) {
- if (attrs[key] !== value[key]) return false;
- }
- return true;
- });
- };
-
- // Convenience version of a common use case of `find`: getting the first object
- // containing specific `key:value` pairs.
- _.findWhere = function(obj, attrs) {
- return _.where(obj, attrs, true);
- };
-
- // Return the maximum element or (element-based computation).
- // Can't optimize arrays of integers longer than 65,535 elements.
- // See: https://bugs.webkit.org/show_bug.cgi?id=80797
- _.max = function(obj, iterator, context) {
- if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) {
- return Math.max.apply(Math, obj);
- }
- if (!iterator && _.isEmpty(obj)) return -Infinity;
- var result = {computed : -Infinity, value: -Infinity};
- each(obj, function(value, index, list) {
- var computed = iterator ? iterator.call(context, value, index, list) : value;
- computed >= result.computed && (result = {value : value, computed : computed});
- });
- return result.value;
- };
-
- // Return the minimum element (or element-based computation).
- _.min = function(obj, iterator, context) {
- if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) {
- return Math.min.apply(Math, obj);
- }
- if (!iterator && _.isEmpty(obj)) return Infinity;
- var result = {computed : Infinity, value: Infinity};
- each(obj, function(value, index, list) {
- var computed = iterator ? iterator.call(context, value, index, list) : value;
- computed < result.computed && (result = {value : value, computed : computed});
- });
- return result.value;
- };
-
- // Shuffle an array.
- _.shuffle = function(obj) {
- var rand;
- var index = 0;
- var shuffled = [];
- each(obj, function(value) {
- rand = _.random(index++);
- shuffled[index - 1] = shuffled[rand];
- shuffled[rand] = value;
- });
- return shuffled;
- };
-
- // An internal function to generate lookup iterators.
- var lookupIterator = function(value) {
- return _.isFunction(value) ? value : function(obj){ return obj[value]; };
- };
-
- // Sort the object's values by a criterion produced by an iterator.
- _.sortBy = function(obj, value, context) {
- var iterator = lookupIterator(value);
- return _.pluck(_.map(obj, function(value, index, list) {
- return {
- value : value,
- index : index,
- criteria : iterator.call(context, value, index, list)
- };
- }).sort(function(left, right) {
- var a = left.criteria;
- var b = right.criteria;
- if (a !== b) {
- if (a > b || a === void 0) return 1;
- if (a < b || b === void 0) return -1;
- }
- return left.index < right.index ? -1 : 1;
- }), 'value');
- };
-
- // An internal function used for aggregate "group by" operations.
- var group = function(obj, value, context, behavior) {
- var result = {};
- var iterator = lookupIterator(value || _.identity);
- each(obj, function(value, index) {
- var key = iterator.call(context, value, index, obj);
- behavior(result, key, value);
- });
- return result;
- };
-
- // Groups the object's values by a criterion. Pass either a string attribute
- // to group by, or a function that returns the criterion.
- _.groupBy = function(obj, value, context) {
- return group(obj, value, context, function(result, key, value) {
- (_.has(result, key) ? result[key] : (result[key] = [])).push(value);
- });
- };
-
- // Counts instances of an object that group by a certain criterion. Pass
- // either a string attribute to count by, or a function that returns the
- // criterion.
- _.countBy = function(obj, value, context) {
- return group(obj, value, context, function(result, key) {
- if (!_.has(result, key)) result[key] = 0;
- result[key]++;
- });
- };
-
- // Use a comparator function to figure out the smallest index at which
- // an object should be inserted so as to maintain order. Uses binary search.
- _.sortedIndex = function(array, obj, iterator, context) {
- iterator = iterator == null ? _.identity : lookupIterator(iterator);
- var value = iterator.call(context, obj);
- var low = 0, high = array.length;
- while (low < high) {
- var mid = (low + high) >>> 1;
- iterator.call(context, array[mid]) < value ? low = mid + 1 : high = mid;
- }
- return low;
- };
-
- // Safely convert anything iterable into a real, live array.
- _.toArray = function(obj) {
- if (!obj) return [];
- if (_.isArray(obj)) return slice.call(obj);
- if (obj.length === +obj.length) return _.map(obj, _.identity);
- return _.values(obj);
- };
-
- // Return the number of elements in an object.
- _.size = function(obj) {
- if (obj == null) return 0;
- return (obj.length === +obj.length) ? obj.length : _.keys(obj).length;
- };
-
- // Array Functions
- // ---------------
-
- // Get the first element of an array. Passing **n** will return the first N
- // values in the array. Aliased as `head` and `take`. The **guard** check
- // allows it to work with `_.map`.
- _.first = _.head = _.take = function(array, n, guard) {
- if (array == null) return void 0;
- return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
- };
-
- // Returns everything but the last entry of the array. Especially useful on
- // the arguments object. Passing **n** will return all the values in
- // the array, excluding the last N. The **guard** check allows it to work with
- // `_.map`.
- _.initial = function(array, n, guard) {
- return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
- };
-
- // Get the last element of an array. Passing **n** will return the last N
- // values in the array. The **guard** check allows it to work with `_.map`.
- _.last = function(array, n, guard) {
- if (array == null) return void 0;
- if ((n != null) && !guard) {
- return slice.call(array, Math.max(array.length - n, 0));
- } else {
- return array[array.length - 1];
- }
- };
-
- // Returns everything but the first entry of the array. Aliased as `tail` and `drop`.
- // Especially useful on the arguments object. Passing an **n** will return
- // the rest N values in the array. The **guard**
- // check allows it to work with `_.map`.
- _.rest = _.tail = _.drop = function(array, n, guard) {
- return slice.call(array, (n == null) || guard ? 1 : n);
- };
-
- // Trim out all falsy values from an array.
- _.compact = function(array) {
- return _.filter(array, _.identity);
- };
-
- // Internal implementation of a recursive `flatten` function.
- var flatten = function(input, shallow, output) {
- each(input, function(value) {
- if (_.isArray(value)) {
- shallow ? push.apply(output, value) : flatten(value, shallow, output);
- } else {
- output.push(value);
- }
- });
- return output;
- };
-
- // Return a completely flattened version of an array.
- _.flatten = function(array, shallow) {
- return flatten(array, shallow, []);
- };
-
- // Return a version of the array that does not contain the specified value(s).
- _.without = function(array) {
- return _.difference(array, slice.call(arguments, 1));
- };
-
- // Produce a duplicate-free version of the array. If the array has already
- // been sorted, you have the option of using a faster algorithm.
- // Aliased as `unique`.
- _.uniq = _.unique = function(array, isSorted, iterator, context) {
- if (_.isFunction(isSorted)) {
- context = iterator;
- iterator = isSorted;
- isSorted = false;
- }
- var initial = iterator ? _.map(array, iterator, context) : array;
- var results = [];
- var seen = [];
- each(initial, function(value, index) {
- if (isSorted ? (!index || seen[seen.length - 1] !== value) : !_.contains(seen, value)) {
- seen.push(value);
- results.push(array[index]);
- }
- });
- return results;
- };
-
- // Produce an array that contains the union: each distinct element from all of
- // the passed-in arrays.
- _.union = function() {
- return _.uniq(concat.apply(ArrayProto, arguments));
- };
-
- // Produce an array that contains every item shared between all the
- // passed-in arrays.
- _.intersection = function(array) {
- var rest = slice.call(arguments, 1);
- return _.filter(_.uniq(array), function(item) {
- return _.every(rest, function(other) {
- return _.indexOf(other, item) >= 0;
- });
- });
- };
-
- // Take the difference between one array and a number of other arrays.
- // Only the elements present in just the first array will remain.
- _.difference = function(array) {
- var rest = concat.apply(ArrayProto, slice.call(arguments, 1));
- return _.filter(array, function(value){ return !_.contains(rest, value); });
- };
-
- // Zip together multiple lists into a single array -- elements that share
- // an index go together.
- _.zip = function() {
- var args = slice.call(arguments);
- var length = _.max(_.pluck(args, 'length'));
- var results = new Array(length);
- for (var i = 0; i < length; i++) {
- results[i] = _.pluck(args, "" + i);
- }
- return results;
- };
-
- // Converts lists into objects. Pass either a single array of `[key, value]`
- // pairs, or two parallel arrays of the same length -- one of keys, and one of
- // the corresponding values.
- _.object = function(list, values) {
- if (list == null) return {};
- var result = {};
- for (var i = 0, l = list.length; i < l; i++) {
- if (values) {
- result[list[i]] = values[i];
- } else {
- result[list[i][0]] = list[i][1];
- }
- }
- return result;
- };
-
- // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
- // we need this function. Return the position of the first occurrence of an
- // item in an array, or -1 if the item is not included in the array.
- // Delegates to **ECMAScript 5**'s native `indexOf` if available.
- // If the array is large and already in sort order, pass `true`
- // for **isSorted** to use binary search.
- _.indexOf = function(array, item, isSorted) {
- if (array == null) return -1;
- var i = 0, l = array.length;
- if (isSorted) {
- if (typeof isSorted == 'number') {
- i = (isSorted < 0 ? Math.max(0, l + isSorted) : isSorted);
- } else {
- i = _.sortedIndex(array, item);
- return array[i] === item ? i : -1;
- }
- }
- if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item, isSorted);
- for (; i < l; i++) if (array[i] === item) return i;
- return -1;
- };
-
- // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
- _.lastIndexOf = function(array, item, from) {
- if (array == null) return -1;
- var hasIndex = from != null;
- if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) {
- return hasIndex ? array.lastIndexOf(item, from) : array.lastIndexOf(item);
- }
- var i = (hasIndex ? from : array.length);
- while (i--) if (array[i] === item) return i;
- return -1;
- };
-
- // Generate an integer Array containing an arithmetic progression. A port of
- // the native Python `range()` function. See
- // [the Python documentation](http://docs.python.org/library/functions.html#range).
- _.range = function(start, stop, step) {
- if (arguments.length <= 1) {
- stop = start || 0;
- start = 0;
- }
- step = arguments[2] || 1;
-
- var len = Math.max(Math.ceil((stop - start) / step), 0);
- var idx = 0;
- var range = new Array(len);
-
- while(idx < len) {
- range[idx++] = start;
- start += step;
- }
-
- return range;
- };
-
- // Function (ahem) Functions
- // ------------------
-
- // Create a function bound to a given object (assigning `this`, and arguments,
- // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if
- // available.
- _.bind = function(func, context) {
- if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
- var args = slice.call(arguments, 2);
- return function() {
- return func.apply(context, args.concat(slice.call(arguments)));
- };
- };
-
- // Partially apply a function by creating a version that has had some of its
- // arguments pre-filled, without changing its dynamic `this` context.
- _.partial = function(func) {
- var args = slice.call(arguments, 1);
- return function() {
- return func.apply(this, args.concat(slice.call(arguments)));
- };
- };
-
- // Bind all of an object's methods to that object. Useful for ensuring that
- // all callbacks defined on an object belong to it.
- _.bindAll = function(obj) {
- var funcs = slice.call(arguments, 1);
- if (funcs.length === 0) funcs = _.functions(obj);
- each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
- return obj;
- };
-
- // Memoize an expensive function by storing its results.
- _.memoize = function(func, hasher) {
- var memo = {};
- hasher || (hasher = _.identity);
- return function() {
- var key = hasher.apply(this, arguments);
- return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
- };
- };
-
- // Delays a function for the given number of milliseconds, and then calls
- // it with the arguments supplied.
- _.delay = function(func, wait) {
- var args = slice.call(arguments, 2);
- return setTimeout(function(){ return func.apply(null, args); }, wait);
- };
-
- // Defers a function, scheduling it to run after the current call stack has
- // cleared.
- _.defer = function(func) {
- return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
- };
-
- // Returns a function, that, when invoked, will only be triggered at most once
- // during a given window of time.
- _.throttle = function(func, wait) {
- var context, args, timeout, result;
- var previous = 0;
- var later = function() {
- previous = new Date;
- timeout = null;
- result = func.apply(context, args);
- };
- return function() {
- var now = new Date;
- var remaining = wait - (now - previous);
- context = this;
- args = arguments;
- if (remaining <= 0) {
- clearTimeout(timeout);
- timeout = null;
- previous = now;
- result = func.apply(context, args);
- } else if (!timeout) {
- timeout = setTimeout(later, remaining);
- }
- return result;
- };
- };
-
- // Returns a function, that, as long as it continues to be invoked, will not
- // be triggered. The function will be called after it stops being called for
- // N milliseconds. If `immediate` is passed, trigger the function on the
- // leading edge, instead of the trailing.
- _.debounce = function(func, wait, immediate) {
- var timeout, result;
- return function() {
- var context = this, args = arguments;
- var later = function() {
- timeout = null;
- if (!immediate) result = func.apply(context, args);
- };
- var callNow = immediate && !timeout;
- clearTimeout(timeout);
- timeout = setTimeout(later, wait);
- if (callNow) result = func.apply(context, args);
- return result;
- };
- };
-
- // Returns a function that will be executed at most one time, no matter how
- // often you call it. Useful for lazy initialization.
- _.once = function(func) {
- var ran = false, memo;
- return function() {
- if (ran) return memo;
- ran = true;
- memo = func.apply(this, arguments);
- func = null;
- return memo;
- };
- };
-
- // Returns the first function passed as an argument to the second,
- // allowing you to adjust arguments, run code before and after, and
- // conditionally execute the original function.
- _.wrap = function(func, wrapper) {
- return function() {
- var args = [func];
- push.apply(args, arguments);
- return wrapper.apply(this, args);
- };
- };
-
- // Returns a function that is the composition of a list of functions, each
- // consuming the return value of the function that follows.
- _.compose = function() {
- var funcs = arguments;
- return function() {
- var args = arguments;
- for (var i = funcs.length - 1; i >= 0; i--) {
- args = [funcs[i].apply(this, args)];
- }
- return args[0];
- };
- };
-
- // Returns a function that will only be executed after being called N times.
- _.after = function(times, func) {
- if (times <= 0) return func();
- return function() {
- if (--times < 1) {
- return func.apply(this, arguments);
- }
- };
- };
-
- // Object Functions
- // ----------------
-
- // Retrieve the names of an object's properties.
- // Delegates to **ECMAScript 5**'s native `Object.keys`
- _.keys = nativeKeys || function(obj) {
- if (obj !== Object(obj)) throw new TypeError('Invalid object');
- var keys = [];
- for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
- return keys;
- };
-
- // Retrieve the values of an object's properties.
- _.values = function(obj) {
- var values = [];
- for (var key in obj) if (_.has(obj, key)) values.push(obj[key]);
- return values;
- };
-
- // Convert an object into a list of `[key, value]` pairs.
- _.pairs = function(obj) {
- var pairs = [];
- for (var key in obj) if (_.has(obj, key)) pairs.push([key, obj[key]]);
- return pairs;
- };
-
- // Invert the keys and values of an object. The values must be serializable.
- _.invert = function(obj) {
- var result = {};
- for (var key in obj) if (_.has(obj, key)) result[obj[key]] = key;
- return result;
- };
-
- // Return a sorted list of the function names available on the object.
- // Aliased as `methods`
- _.functions = _.methods = function(obj) {
- var names = [];
- for (var key in obj) {
- if (_.isFunction(obj[key])) names.push(key);
- }
- return names.sort();
- };
-
- // Extend a given object with all the properties in passed-in object(s).
- _.extend = function(obj) {
- each(slice.call(arguments, 1), function(source) {
- if (source) {
- for (var prop in source) {
- obj[prop] = source[prop];
- }
- }
- });
- return obj;
- };
-
- // Return a copy of the object only containing the whitelisted properties.
- _.pick = function(obj) {
- var copy = {};
- var keys = concat.apply(ArrayProto, slice.call(arguments, 1));
- each(keys, function(key) {
- if (key in obj) copy[key] = obj[key];
- });
- return copy;
- };
-
- // Return a copy of the object without the blacklisted properties.
- _.omit = function(obj) {
- var copy = {};
- var keys = concat.apply(ArrayProto, slice.call(arguments, 1));
- for (var key in obj) {
- if (!_.contains(keys, key)) copy[key] = obj[key];
- }
- return copy;
- };
-
- // Fill in a given object with default properties.
- _.defaults = function(obj) {
- each(slice.call(arguments, 1), function(source) {
- if (source) {
- for (var prop in source) {
- if (obj[prop] == null) obj[prop] = source[prop];
- }
- }
- });
- return obj;
- };
-
- // Create a (shallow-cloned) duplicate of an object.
- _.clone = function(obj) {
- if (!_.isObject(obj)) return obj;
- return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
- };
-
- // Invokes interceptor with the obj, and then returns obj.
- // The primary purpose of this method is to "tap into" a method chain, in
- // order to perform operations on intermediate results within the chain.
- _.tap = function(obj, interceptor) {
- interceptor(obj);
- return obj;
- };
-
- // Internal recursive comparison function for `isEqual`.
- var eq = function(a, b, aStack, bStack) {
- // Identical objects are equal. `0 === -0`, but they aren't identical.
- // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
- if (a === b) return a !== 0 || 1 / a == 1 / b;
- // A strict comparison is necessary because `null == undefined`.
- if (a == null || b == null) return a === b;
- // Unwrap any wrapped objects.
- if (a instanceof _) a = a._wrapped;
- if (b instanceof _) b = b._wrapped;
- // Compare `[[Class]]` names.
- var className = toString.call(a);
- if (className != toString.call(b)) return false;
- switch (className) {
- // Strings, numbers, dates, and booleans are compared by value.
- case '[object String]':
- // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
- // equivalent to `new String("5")`.
- return a == String(b);
- case '[object Number]':
- // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
- // other numeric values.
- return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
- case '[object Date]':
- case '[object Boolean]':
- // Coerce dates and booleans to numeric primitive values. Dates are compared by their
- // millisecond representations. Note that invalid dates with millisecond representations
- // of `NaN` are not equivalent.
- return +a == +b;
- // RegExps are compared by their source patterns and flags.
- case '[object RegExp]':
- return a.source == b.source &&
- a.global == b.global &&
- a.multiline == b.multiline &&
- a.ignoreCase == b.ignoreCase;
- }
- if (typeof a != 'object' || typeof b != 'object') return false;
- // Assume equality for cyclic structures. The algorithm for detecting cyclic
- // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
- var length = aStack.length;
- while (length--) {
- // Linear search. Performance is inversely proportional to the number of
- // unique nested structures.
- if (aStack[length] == a) return bStack[length] == b;
- }
- // Add the first object to the stack of traversed objects.
- aStack.push(a);
- bStack.push(b);
- var size = 0, result = true;
- // Recursively compare objects and arrays.
- if (className == '[object Array]') {
- // Compare array lengths to determine if a deep comparison is necessary.
- size = a.length;
- result = size == b.length;
- if (result) {
- // Deep compare the contents, ignoring non-numeric properties.
- while (size--) {
- if (!(result = eq(a[size], b[size], aStack, bStack))) break;
- }
- }
- } else {
- // Objects with different constructors are not equivalent, but `Object`s
- // from different frames are.
- var aCtor = a.constructor, bCtor = b.constructor;
- if (aCtor !== bCtor && !(_.isFunction(aCtor) && (aCtor instanceof aCtor) &&
- _.isFunction(bCtor) && (bCtor instanceof bCtor))) {
- return false;
- }
- // Deep compare objects.
- for (var key in a) {
- if (_.has(a, key)) {
- // Count the expected number of properties.
- size++;
- // Deep compare each member.
- if (!(result = _.has(b, key) && eq(a[key], b[key], aStack, bStack))) break;
- }
- }
- // Ensure that both objects contain the same number of properties.
- if (result) {
- for (key in b) {
- if (_.has(b, key) && !(size--)) break;
- }
- result = !size;
- }
- }
- // Remove the first object from the stack of traversed objects.
- aStack.pop();
- bStack.pop();
- return result;
- };
-
- // Perform a deep comparison to check if two objects are equal.
- _.isEqual = function(a, b) {
- return eq(a, b, [], []);
- };
-
- // Is a given array, string, or object empty?
- // An "empty" object has no enumerable own-properties.
- _.isEmpty = function(obj) {
- if (obj == null) return true;
- if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
- for (var key in obj) if (_.has(obj, key)) return false;
- return true;
- };
-
- // Is a given value a DOM element?
- _.isElement = function(obj) {
- return !!(obj && obj.nodeType === 1);
- };
-
- // Is a given value an array?
- // Delegates to ECMA5's native Array.isArray
- _.isArray = nativeIsArray || function(obj) {
- return toString.call(obj) == '[object Array]';
- };
-
- // Is a given variable an object?
- _.isObject = function(obj) {
- return obj === Object(obj);
- };
-
- // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp.
- each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp'], function(name) {
- _['is' + name] = function(obj) {
- return toString.call(obj) == '[object ' + name + ']';
- };
- });
-
- // Define a fallback version of the method in browsers (ahem, IE), where
- // there isn't any inspectable "Arguments" type.
- if (!_.isArguments(arguments)) {
- _.isArguments = function(obj) {
- return !!(obj && _.has(obj, 'callee'));
- };
- }
-
- // Optimize `isFunction` if appropriate.
- if (typeof (/./) !== 'function') {
- _.isFunction = function(obj) {
- return typeof obj === 'function';
- };
- }
-
- // Is a given object a finite number?
- _.isFinite = function(obj) {
- return isFinite(obj) && !isNaN(parseFloat(obj));
- };
-
- // Is the given value `NaN`? (NaN is the only number which does not equal itself).
- _.isNaN = function(obj) {
- return _.isNumber(obj) && obj != +obj;
- };
-
- // Is a given value a boolean?
- _.isBoolean = function(obj) {
- return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
- };
-
- // Is a given value equal to null?
- _.isNull = function(obj) {
- return obj === null;
- };
-
- // Is a given variable undefined?
- _.isUndefined = function(obj) {
- return obj === void 0;
- };
-
- // Shortcut function for checking if an object has a given property directly
- // on itself (in other words, not on a prototype).
- _.has = function(obj, key) {
- return hasOwnProperty.call(obj, key);
- };
-
- // Utility Functions
- // -----------------
-
- // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
- // previous owner. Returns a reference to the Underscore object.
- _.noConflict = function() {
- root._ = previousUnderscore;
- return this;
- };
-
- // Keep the identity function around for default iterators.
- _.identity = function(value) {
- return value;
- };
-
- // Run a function **n** times.
- _.times = function(n, iterator, context) {
- var accum = Array(n);
- for (var i = 0; i < n; i++) accum[i] = iterator.call(context, i);
- return accum;
- };
-
- // Return a random integer between min and max (inclusive).
- _.random = function(min, max) {
- if (max == null) {
- max = min;
- min = 0;
- }
- return min + Math.floor(Math.random() * (max - min + 1));
- };
-
- // List of HTML entities for escaping.
- var entityMap = {
- escape: {
- '&': '&',
- '<': '<',
- '>': '>',
- '"': '"',
- "'": ''',
- '/': '/'
- }
- };
- entityMap.unescape = _.invert(entityMap.escape);
-
- // Regexes containing the keys and values listed immediately above.
- var entityRegexes = {
- escape: new RegExp('[' + _.keys(entityMap.escape).join('') + ']', 'g'),
- unescape: new RegExp('(' + _.keys(entityMap.unescape).join('|') + ')', 'g')
- };
-
- // Functions for escaping and unescaping strings to/from HTML interpolation.
- _.each(['escape', 'unescape'], function(method) {
- _[method] = function(string) {
- if (string == null) return '';
- return ('' + string).replace(entityRegexes[method], function(match) {
- return entityMap[method][match];
- });
- };
- });
-
- // If the value of the named property is a function then invoke it;
- // otherwise, return it.
- _.result = function(object, property) {
- if (object == null) return null;
- var value = object[property];
- return _.isFunction(value) ? value.call(object) : value;
- };
-
- // Add your own custom functions to the Underscore object.
- _.mixin = function(obj) {
- each(_.functions(obj), function(name){
- var func = _[name] = obj[name];
- _.prototype[name] = function() {
- var args = [this._wrapped];
- push.apply(args, arguments);
- return result.call(this, func.apply(_, args));
- };
- });
- };
-
- // Generate a unique integer id (unique within the entire client session).
- // Useful for temporary DOM ids.
- var idCounter = 0;
- _.uniqueId = function(prefix) {
- var id = ++idCounter + '';
- return prefix ? prefix + id : id;
- };
-
- // By default, Underscore uses ERB-style template delimiters, change the
- // following template settings to use alternative delimiters.
- _.templateSettings = {
- evaluate : /<%([\s\S]+?)%>/g,
- interpolate : /<%=([\s\S]+?)%>/g,
- escape : /<%-([\s\S]+?)%>/g
- };
-
- // When customizing `templateSettings`, if you don't want to define an
- // interpolation, evaluation or escaping regex, we need one that is
- // guaranteed not to match.
- var noMatch = /(.)^/;
-
- // Certain characters need to be escaped so that they can be put into a
- // string literal.
- var escapes = {
- "'": "'",
- '\\': '\\',
- '\r': 'r',
- '\n': 'n',
- '\t': 't',
- '\u2028': 'u2028',
- '\u2029': 'u2029'
- };
-
- var escaper = /\\|'|\r|\n|\t|\u2028|\u2029/g;
-
- // JavaScript micro-templating, similar to John Resig's implementation.
- // Underscore templating handles arbitrary delimiters, preserves whitespace,
- // and correctly escapes quotes within interpolated code.
- _.template = function(text, data, settings) {
- var render;
- settings = _.defaults({}, settings, _.templateSettings);
-
- // Combine delimiters into one regular expression via alternation.
- var matcher = new RegExp([
- (settings.escape || noMatch).source,
- (settings.interpolate || noMatch).source,
- (settings.evaluate || noMatch).source
- ].join('|') + '|$', 'g');
-
- // Compile the template source, escaping string literals appropriately.
- var index = 0;
- var source = "__p+='";
- text.replace(matcher, function(match, escape, interpolate, evaluate, offset) {
- source += text.slice(index, offset)
- .replace(escaper, function(match) { return '\\' + escapes[match]; });
-
- if (escape) {
- source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'";
- }
- if (interpolate) {
- source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'";
- }
- if (evaluate) {
- source += "';\n" + evaluate + "\n__p+='";
- }
- index = offset + match.length;
- return match;
- });
- source += "';\n";
-
- // If a variable is not specified, place data values in local scope.
- if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n';
-
- source = "var __t,__p='',__j=Array.prototype.join," +
- "print=function(){__p+=__j.call(arguments,'');};\n" +
- source + "return __p;\n";
-
- try {
- render = new Function(settings.variable || 'obj', '_', source);
- } catch (e) {
- e.source = source;
- throw e;
- }
-
- if (data) return render(data, _);
- var template = function(data) {
- return render.call(this, data, _);
- };
-
- // Provide the compiled function source as a convenience for precompilation.
- template.source = 'function(' + (settings.variable || 'obj') + '){\n' + source + '}';
-
- return template;
- };
-
- // Add a "chain" function, which will delegate to the wrapper.
- _.chain = function(obj) {
- return _(obj).chain();
- };
-
- // OOP
- // ---------------
- // If Underscore is called as a function, it returns a wrapped object that
- // can be used OO-style. This wrapper holds altered versions of all the
- // underscore functions. Wrapped objects may be chained.
-
- // Helper function to continue chaining intermediate results.
- var result = function(obj) {
- return this._chain ? _(obj).chain() : obj;
- };
-
- // Add all of the Underscore functions to the wrapper object.
- _.mixin(_);
-
- // Add all mutator Array functions to the wrapper.
- each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
- var method = ArrayProto[name];
- _.prototype[name] = function() {
- var obj = this._wrapped;
- method.apply(obj, arguments);
- if ((name == 'shift' || name == 'splice') && obj.length === 0) delete obj[0];
- return result.call(this, obj);
- };
- });
-
- // Add all accessor Array functions to the wrapper.
- each(['concat', 'join', 'slice'], function(name) {
- var method = ArrayProto[name];
- _.prototype[name] = function() {
- return result.call(this, method.apply(this._wrapped, arguments));
- };
- });
-
- _.extend(_.prototype, {
-
- // Start chaining a wrapped Underscore object.
- chain: function() {
- this._chain = true;
- return this;
- },
-
- // Extracts the result from a wrapped and chained object.
- value: function() {
- return this._wrapped;
- }
-
- });
-
-}).call(this);
diff --git a/moose-core/Docs/user/html/pymoose/_static/up-pressed.png b/moose-core/Docs/user/html/pymoose/_static/up-pressed.png
deleted file mode 100644
index 8bd587afee2fe38989383ff82010147ea56b93dd..0000000000000000000000000000000000000000
Binary files a/moose-core/Docs/user/html/pymoose/_static/up-pressed.png and /dev/null differ
diff --git a/moose-core/Docs/user/html/pymoose/_static/up.png b/moose-core/Docs/user/html/pymoose/_static/up.png
deleted file mode 100644
index b94625680b4a4b9647c3a6f3f283776930696aa9..0000000000000000000000000000000000000000
Binary files a/moose-core/Docs/user/html/pymoose/_static/up.png and /dev/null differ
diff --git a/moose-core/Docs/user/html/pymoose/_static/websupport.js b/moose-core/Docs/user/html/pymoose/_static/websupport.js
deleted file mode 100644
index e9bd1b851c62bf625a2cac10d8da09526c440373..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/html/pymoose/_static/websupport.js
+++ /dev/null
@@ -1,808 +0,0 @@
-/*
- * websupport.js
- * ~~~~~~~~~~~~~
- *
- * sphinx.websupport utilties for all documentation.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-(function($) {
- $.fn.autogrow = function() {
- return this.each(function() {
- var textarea = this;
-
- $.fn.autogrow.resize(textarea);
-
- $(textarea)
- .focus(function() {
- textarea.interval = setInterval(function() {
- $.fn.autogrow.resize(textarea);
- }, 500);
- })
- .blur(function() {
- clearInterval(textarea.interval);
- });
- });
- };
-
- $.fn.autogrow.resize = function(textarea) {
- var lineHeight = parseInt($(textarea).css('line-height'), 10);
- var lines = textarea.value.split('\n');
- var columns = textarea.cols;
- var lineCount = 0;
- $.each(lines, function() {
- lineCount += Math.ceil(this.length / columns) || 1;
- });
- var height = lineHeight * (lineCount + 1);
- $(textarea).css('height', height);
- };
-})(jQuery);
-
-(function($) {
- var comp, by;
-
- function init() {
- initEvents();
- initComparator();
- }
-
- function initEvents() {
- $('a.comment-close').live("click", function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- });
- $('a.vote').live("click", function(event) {
- event.preventDefault();
- handleVote($(this));
- });
- $('a.reply').live("click", function(event) {
- event.preventDefault();
- openReply($(this).attr('id').substring(2));
- });
- $('a.close-reply').live("click", function(event) {
- event.preventDefault();
- closeReply($(this).attr('id').substring(2));
- });
- $('a.sort-option').live("click", function(event) {
- event.preventDefault();
- handleReSort($(this));
- });
- $('a.show-proposal').live("click", function(event) {
- event.preventDefault();
- showProposal($(this).attr('id').substring(2));
- });
- $('a.hide-proposal').live("click", function(event) {
- event.preventDefault();
- hideProposal($(this).attr('id').substring(2));
- });
- $('a.show-propose-change').live("click", function(event) {
- event.preventDefault();
- showProposeChange($(this).attr('id').substring(2));
- });
- $('a.hide-propose-change').live("click", function(event) {
- event.preventDefault();
- hideProposeChange($(this).attr('id').substring(2));
- });
- $('a.accept-comment').live("click", function(event) {
- event.preventDefault();
- acceptComment($(this).attr('id').substring(2));
- });
- $('a.delete-comment').live("click", function(event) {
- event.preventDefault();
- deleteComment($(this).attr('id').substring(2));
- });
- $('a.comment-markup').live("click", function(event) {
- event.preventDefault();
- toggleCommentMarkupBox($(this).attr('id').substring(2));
- });
- }
-
- /**
- * Set comp, which is a comparator function used for sorting and
- * inserting comments into the list.
- */
- function setComparator() {
- // If the first three letters are "asc", sort in ascending order
- // and remove the prefix.
- if (by.substring(0,3) == 'asc') {
- var i = by.substring(3);
- comp = function(a, b) { return a[i] - b[i]; };
- } else {
- // Otherwise sort in descending order.
- comp = function(a, b) { return b[by] - a[by]; };
- }
-
- // Reset link styles and format the selected sort option.
- $('a.sel').attr('href', '#').removeClass('sel');
- $('a.by' + by).removeAttr('href').addClass('sel');
- }
-
- /**
- * Create a comp function. If the user has preferences stored in
- * the sortBy cookie, use those, otherwise use the default.
- */
- function initComparator() {
- by = 'rating'; // Default to sort by rating.
- // If the sortBy cookie is set, use that instead.
- if (document.cookie.length > 0) {
- var start = document.cookie.indexOf('sortBy=');
- if (start != -1) {
- start = start + 7;
- var end = document.cookie.indexOf(";", start);
- if (end == -1) {
- end = document.cookie.length;
- by = unescape(document.cookie.substring(start, end));
- }
- }
- }
- setComparator();
- }
-
- /**
- * Show a comment div.
- */
- function show(id) {
- $('#ao' + id).hide();
- $('#ah' + id).show();
- var context = $.extend({id: id}, opts);
- var popup = $(renderTemplate(popupTemplate, context)).hide();
- popup.find('textarea[name="proposal"]').hide();
- popup.find('a.by' + by).addClass('sel');
- var form = popup.find('#cf' + id);
- form.submit(function(event) {
- event.preventDefault();
- addComment(form);
- });
- $('#s' + id).after(popup);
- popup.slideDown('fast', function() {
- getComments(id);
- });
- }
-
- /**
- * Hide a comment div.
- */
- function hide(id) {
- $('#ah' + id).hide();
- $('#ao' + id).show();
- var div = $('#sc' + id);
- div.slideUp('fast', function() {
- div.remove();
- });
- }
-
- /**
- * Perform an ajax request to get comments for a node
- * and insert the comments into the comments tree.
- */
- function getComments(id) {
- $.ajax({
- type: 'GET',
- url: opts.getCommentsURL,
- data: {node: id},
- success: function(data, textStatus, request) {
- var ul = $('#cl' + id);
- var speed = 100;
- $('#cf' + id)
- .find('textarea[name="proposal"]')
- .data('source', data.source);
-
- if (data.comments.length === 0) {
- ul.html('<li>No comments yet.</li>');
- ul.data('empty', true);
- } else {
- // If there are comments, sort them and put them in the list.
- var comments = sortComments(data.comments);
- speed = data.comments.length * 100;
- appendComments(comments, ul);
- ul.data('empty', false);
- }
- $('#cn' + id).slideUp(speed + 200);
- ul.slideDown(speed);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem retrieving the comments.');
- },
- dataType: 'json'
- });
- }
-
- /**
- * Add a comment via ajax and insert the comment into the comment tree.
- */
- function addComment(form) {
- var node_id = form.find('input[name="node"]').val();
- var parent_id = form.find('input[name="parent"]').val();
- var text = form.find('textarea[name="comment"]').val();
- var proposal = form.find('textarea[name="proposal"]').val();
-
- if (text == '') {
- showError('Please enter a comment.');
- return;
- }
-
- // Disable the form that is being submitted.
- form.find('textarea,input').attr('disabled', 'disabled');
-
- // Send the comment to the server.
- $.ajax({
- type: "POST",
- url: opts.addCommentURL,
- dataType: 'json',
- data: {
- node: node_id,
- parent: parent_id,
- text: text,
- proposal: proposal
- },
- success: function(data, textStatus, error) {
- // Reset the form.
- if (node_id) {
- hideProposeChange(node_id);
- }
- form.find('textarea')
- .val('')
- .add(form.find('input'))
- .removeAttr('disabled');
- var ul = $('#cl' + (node_id || parent_id));
- if (ul.data('empty')) {
- $(ul).empty();
- ul.data('empty', false);
- }
- insertComment(data.comment);
- var ao = $('#ao' + node_id);
- ao.find('img').attr({'src': opts.commentBrightImage});
- if (node_id) {
- // if this was a "root" comment, remove the commenting box
- // (the user can get it back by reopening the comment popup)
- $('#ca' + node_id).slideUp();
- }
- },
- error: function(request, textStatus, error) {
- form.find('textarea,input').removeAttr('disabled');
- showError('Oops, there was a problem adding the comment.');
- }
- });
- }
-
- /**
- * Recursively append comments to the main comment list and children
- * lists, creating the comment tree.
- */
- function appendComments(comments, ul) {
- $.each(comments, function() {
- var div = createCommentDiv(this);
- ul.append($(document.createElement('li')).html(div));
- appendComments(this.children, div.find('ul.comment-children'));
- // To avoid stagnating data, don't store the comments children in data.
- this.children = null;
- div.data('comment', this);
- });
- }
-
- /**
- * After adding a new comment, it must be inserted in the correct
- * location in the comment tree.
- */
- function insertComment(comment) {
- var div = createCommentDiv(comment);
-
- // To avoid stagnating data, don't store the comments children in data.
- comment.children = null;
- div.data('comment', comment);
-
- var ul = $('#cl' + (comment.node || comment.parent));
- var siblings = getChildren(ul);
-
- var li = $(document.createElement('li'));
- li.hide();
-
- // Determine where in the parents children list to insert this comment.
- for(i=0; i < siblings.length; i++) {
- if (comp(comment, siblings[i]) <= 0) {
- $('#cd' + siblings[i].id)
- .parent()
- .before(li.html(div));
- li.slideDown('fast');
- return;
- }
- }
-
- // If we get here, this comment rates lower than all the others,
- // or it is the only comment in the list.
- ul.append(li.html(div));
- li.slideDown('fast');
- }
-
- function acceptComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.acceptCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- $('#cm' + id).fadeOut('fast');
- $('#cd' + id).removeClass('moderate');
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem accepting the comment.');
- }
- });
- }
-
- function deleteComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.deleteCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- var div = $('#cd' + id);
- if (data == 'delete') {
- // Moderator mode: remove the comment and all children immediately
- div.slideUp('fast', function() {
- div.remove();
- });
- return;
- }
- // User mode: only mark the comment as deleted
- div
- .find('span.user-id:first')
- .text('[deleted]').end()
- .find('div.comment-text:first')
- .text('[deleted]').end()
- .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
- ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
- .remove();
- var comment = div.data('comment');
- comment.username = '[deleted]';
- comment.text = '[deleted]';
- div.data('comment', comment);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem deleting the comment.');
- }
- });
- }
-
- function showProposal(id) {
- $('#sp' + id).hide();
- $('#hp' + id).show();
- $('#pr' + id).slideDown('fast');
- }
-
- function hideProposal(id) {
- $('#hp' + id).hide();
- $('#sp' + id).show();
- $('#pr' + id).slideUp('fast');
- }
-
- function showProposeChange(id) {
- $('#pc' + id).hide();
- $('#hc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val(textarea.data('source'));
- $.fn.autogrow.resize(textarea[0]);
- textarea.slideDown('fast');
- }
-
- function hideProposeChange(id) {
- $('#hc' + id).hide();
- $('#pc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val('').removeAttr('disabled');
- textarea.slideUp('fast');
- }
-
- function toggleCommentMarkupBox(id) {
- $('#mb' + id).toggle();
- }
-
- /** Handle when the user clicks on a sort by link. */
- function handleReSort(link) {
- var classes = link.attr('class').split(/\s+/);
- for (var i=0; i<classes.length; i++) {
- if (classes[i] != 'sort-option') {
- by = classes[i].substring(2);
- }
- }
- setComparator();
- // Save/update the sortBy cookie.
- var expiration = new Date();
- expiration.setDate(expiration.getDate() + 365);
- document.cookie= 'sortBy=' + escape(by) +
- ';expires=' + expiration.toUTCString();
- $('ul.comment-ul').each(function(index, ul) {
- var comments = getChildren($(ul), true);
- comments = sortComments(comments);
- appendComments(comments, $(ul).empty());
- });
- }
-
- /**
- * Function to process a vote when a user clicks an arrow.
- */
- function handleVote(link) {
- if (!opts.voting) {
- showError("You'll need to login to vote.");
- return;
- }
-
- var id = link.attr('id');
- if (!id) {
- // Didn't click on one of the voting arrows.
- return;
- }
- // If it is an unvote, the new vote value is 0,
- // Otherwise it's 1 for an upvote, or -1 for a downvote.
- var value = 0;
- if (id.charAt(1) != 'u') {
- value = id.charAt(0) == 'u' ? 1 : -1;
- }
- // The data to be sent to the server.
- var d = {
- comment_id: id.substring(2),
- value: value
- };
-
- // Swap the vote and unvote links.
- link.hide();
- $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
- .show();
-
- // The div the comment is displayed in.
- var div = $('div#cd' + d.comment_id);
- var data = div.data('comment');
-
- // If this is not an unvote, and the other vote arrow has
- // already been pressed, unpress it.
- if ((d.value !== 0) && (data.vote === d.value * -1)) {
- $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
- $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
- }
-
- // Update the comments rating in the local data.
- data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
- data.vote = d.value;
- div.data('comment', data);
-
- // Change the rating text.
- div.find('.rating:first')
- .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
-
- // Send the vote information to the server.
- $.ajax({
- type: "POST",
- url: opts.processVoteURL,
- data: d,
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem casting that vote.');
- }
- });
- }
-
- /**
- * Open a reply form used to reply to an existing comment.
- */
- function openReply(id) {
- // Swap out the reply link for the hide link
- $('#rl' + id).hide();
- $('#cr' + id).show();
-
- // Add the reply li to the children ul.
- var div = $(renderTemplate(replyTemplate, {id: id})).hide();
- $('#cl' + id)
- .prepend(div)
- // Setup the submit handler for the reply form.
- .find('#rf' + id)
- .submit(function(event) {
- event.preventDefault();
- addComment($('#rf' + id));
- closeReply(id);
- })
- .find('input[type=button]')
- .click(function() {
- closeReply(id);
- });
- div.slideDown('fast', function() {
- $('#rf' + id).find('textarea').focus();
- });
- }
-
- /**
- * Close the reply form opened with openReply.
- */
- function closeReply(id) {
- // Remove the reply div from the DOM.
- $('#rd' + id).slideUp('fast', function() {
- $(this).remove();
- });
-
- // Swap out the hide link for the reply link
- $('#cr' + id).hide();
- $('#rl' + id).show();
- }
-
- /**
- * Recursively sort a tree of comments using the comp comparator.
- */
- function sortComments(comments) {
- comments.sort(comp);
- $.each(comments, function() {
- this.children = sortComments(this.children);
- });
- return comments;
- }
-
- /**
- * Get the children comments from a ul. If recursive is true,
- * recursively include childrens' children.
- */
- function getChildren(ul, recursive) {
- var children = [];
- ul.children().children("[id^='cd']")
- .each(function() {
- var comment = $(this).data('comment');
- if (recursive)
- comment.children = getChildren($(this).find('#cl' + comment.id), true);
- children.push(comment);
- });
- return children;
- }
-
- /** Create a div to display a comment in. */
- function createCommentDiv(comment) {
- if (!comment.displayed && !opts.moderator) {
- return $('<div class="moderate">Thank you! Your comment will show up '
- + 'once it is has been approved by a moderator.</div>');
- }
- // Prettify the comment rating.
- comment.pretty_rating = comment.rating + ' point' +
- (comment.rating == 1 ? '' : 's');
- // Make a class (for displaying not yet moderated comments differently)
- comment.css_class = comment.displayed ? '' : ' moderate';
- // Create a div for this comment.
- var context = $.extend({}, opts, comment);
- var div = $(renderTemplate(commentTemplate, context));
-
- // If the user has voted on this comment, highlight the correct arrow.
- if (comment.vote) {
- var direction = (comment.vote == 1) ? 'u' : 'd';
- div.find('#' + direction + 'v' + comment.id).hide();
- div.find('#' + direction + 'u' + comment.id).show();
- }
-
- if (opts.moderator || comment.text != '[deleted]') {
- div.find('a.reply').show();
- if (comment.proposal_diff)
- div.find('#sp' + comment.id).show();
- if (opts.moderator && !comment.displayed)
- div.find('#cm' + comment.id).show();
- if (opts.moderator || (opts.username == comment.username))
- div.find('#dc' + comment.id).show();
- }
- return div;
- }
-
- /**
- * A simple template renderer. Placeholders such as <%id%> are replaced
- * by context['id'] with items being escaped. Placeholders such as <#id#>
- * are not escaped.
- */
- function renderTemplate(template, context) {
- var esc = $(document.createElement('div'));
-
- function handle(ph, escape) {
- var cur = context;
- $.each(ph.split('.'), function() {
- cur = cur[this];
- });
- return escape ? esc.text(cur || "").html() : cur;
- }
-
- return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
- return handle(arguments[2], arguments[1] == '%' ? true : false);
- });
- }
-
- /** Flash an error message briefly. */
- function showError(message) {
- $(document.createElement('div')).attr({'class': 'popup-error'})
- .append($(document.createElement('div'))
- .attr({'class': 'error-message'}).text(message))
- .appendTo('body')
- .fadeIn("slow")
- .delay(2000)
- .fadeOut("slow");
- }
-
- /** Add a link the user uses to open the comments popup. */
- $.fn.comment = function() {
- return this.each(function() {
- var id = $(this).attr('id').substring(1);
- var count = COMMENT_METADATA[id];
- var title = count + ' comment' + (count == 1 ? '' : 's');
- var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
- var addcls = count == 0 ? ' nocomment' : '';
- $(this)
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-open' + addcls,
- id: 'ao' + id
- })
- .append($(document.createElement('img')).attr({
- src: image,
- alt: 'comment',
- title: title
- }))
- .click(function(event) {
- event.preventDefault();
- show($(this).attr('id').substring(2));
- })
- )
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-close hidden',
- id: 'ah' + id
- })
- .append($(document.createElement('img')).attr({
- src: opts.closeCommentImage,
- alt: 'close',
- title: 'close'
- }))
- .click(function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- })
- );
- });
- };
-
- var opts = {
- processVoteURL: '/_process_vote',
- addCommentURL: '/_add_comment',
- getCommentsURL: '/_get_comments',
- acceptCommentURL: '/_accept_comment',
- deleteCommentURL: '/_delete_comment',
- commentImage: '/static/_static/comment.png',
- closeCommentImage: '/static/_static/comment-close.png',
- loadingImage: '/static/_static/ajax-loader.gif',
- commentBrightImage: '/static/_static/comment-bright.png',
- upArrow: '/static/_static/up.png',
- downArrow: '/static/_static/down.png',
- upArrowPressed: '/static/_static/up-pressed.png',
- downArrowPressed: '/static/_static/down-pressed.png',
- voting: false,
- moderator: false
- };
-
- if (typeof COMMENT_OPTIONS != "undefined") {
- opts = jQuery.extend(opts, COMMENT_OPTIONS);
- }
-
- var popupTemplate = '\
- <div class="sphinx-comments" id="sc<%id%>">\
- <p class="sort-options">\
- Sort by:\
- <a href="#" class="sort-option byrating">best rated</a>\
- <a href="#" class="sort-option byascage">newest</a>\
- <a href="#" class="sort-option byage">oldest</a>\
- </p>\
- <div class="comment-header">Comments</div>\
- <div class="comment-loading" id="cn<%id%>">\
- loading comments... <img src="<%loadingImage%>" alt="" /></div>\
- <ul id="cl<%id%>" class="comment-ul"></ul>\
- <div id="ca<%id%>">\
- <p class="add-a-comment">Add a comment\
- (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
- <div class="comment-markup-box" id="mb<%id%>">\
- reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
- <tt>``code``</tt>, \
- code blocks: <tt>::</tt> and an indented block after blank line</div>\
- <form method="post" id="cf<%id%>" class="comment-form" action="">\
- <textarea name="comment" cols="80"></textarea>\
- <p class="propose-button">\
- <a href="#" id="pc<%id%>" class="show-propose-change">\
- Propose a change ▹\
- </a>\
- <a href="#" id="hc<%id%>" class="hide-propose-change">\
- Propose a change ▿\
- </a>\
- </p>\
- <textarea name="proposal" id="pt<%id%>" cols="80"\
- spellcheck="false"></textarea>\
- <input type="submit" value="Add comment" />\
- <input type="hidden" name="node" value="<%id%>" />\
- <input type="hidden" name="parent" value="" />\
- </form>\
- </div>\
- </div>';
-
- var commentTemplate = '\
- <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
- <div class="vote">\
- <div class="arrow">\
- <a href="#" id="uv<%id%>" class="vote" title="vote up">\
- <img src="<%upArrow%>" />\
- </a>\
- <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
- <img src="<%upArrowPressed%>" />\
- </a>\
- </div>\
- <div class="arrow">\
- <a href="#" id="dv<%id%>" class="vote" title="vote down">\
- <img src="<%downArrow%>" id="da<%id%>" />\
- </a>\
- <a href="#" id="du<%id%>" class="un vote" title="vote down">\
- <img src="<%downArrowPressed%>" />\
- </a>\
- </div>\
- </div>\
- <div class="comment-content">\
- <p class="tagline comment">\
- <span class="user-id"><%username%></span>\
- <span class="rating"><%pretty_rating%></span>\
- <span class="delta"><%time.delta%></span>\
- </p>\
- <div class="comment-text comment"><#text#></div>\
- <p class="comment-opts comment">\
- <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\
- <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\
- <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\
- <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\
- <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
- <span id="cm<%id%>" class="moderation hidden">\
- <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
- </span>\
- </p>\
- <pre class="proposal" id="pr<%id%>">\
-<#proposal_diff#>\
- </pre>\
- <ul class="comment-children" id="cl<%id%>"></ul>\
- </div>\
- <div class="clearleft"></div>\
- </div>\
- </div>';
-
- var replyTemplate = '\
- <li>\
- <div class="reply-div" id="rd<%id%>">\
- <form id="rf<%id%>">\
- <textarea name="comment" cols="80"></textarea>\
- <input type="submit" value="Add reply" />\
- <input type="button" value="Cancel" />\
- <input type="hidden" name="parent" value="<%id%>" />\
- <input type="hidden" name="node" value="" />\
- </form>\
- </div>\
- </li>';
-
- $(document).ready(function() {
- init();
- });
-})(jQuery);
-
-$(document).ready(function() {
- // add comment anchors for all paragraphs that are commentable
- $('.sphinx-has-comment').comment();
-
- // highlight search words in search results
- $("div.context").each(function() {
- var params = $.getQueryParameters();
- var terms = (params.q) ? params.q[0].split(/\s+/) : [];
- var result = $(this);
- $.each(terms, function() {
- result.highlightText(this.toLowerCase(), 'highlighted');
- });
- });
-
- // directly open comment window if requested
- var anchor = document.location.hash;
- if (anchor.substring(0, 9) == '#comment-') {
- $('#ao' + anchor.substring(9)).click();
- document.location.hash = '#s' + anchor.substring(9);
- }
-});
diff --git a/moose-core/Docs/user/html/pymoose/genindex.html b/moose-core/Docs/user/html/pymoose/genindex.html
deleted file mode 100644
index 6a097a5d93b81d78809177571f3b7329e5845dbe..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/html/pymoose/genindex.html
+++ /dev/null
@@ -1,8413 +0,0 @@
-
-
-
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Index — MOOSE 3.0 documentation</title>
-
- <link rel="stylesheet" href="_static/default.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '',
- VERSION: '3.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
- <script type="text/javascript" src="_static/jquery.js"></script>
- <script type="text/javascript" src="_static/underscore.js"></script>
- <script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="MOOSE 3.0 documentation" href="index.html" />
- </head>
- <body>
- <div class="related">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="#" title="General Index"
- accesskey="I">index</a></li>
- <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li>
-
- <li><a href="index.html">MOOSE 3.0 documentation</a> »</li>
-
- </ul>
- </div>
-
- <div class="document">
- <div class="documentwrapper">
- <div class="bodywrapper">
- <div class="body">
-
-
-<h1 id="index">Index</h1>
-
-<div class="genindex-jumpbox">
- <a href="#A"><strong>A</strong></a>
- | <a href="#B"><strong>B</strong></a>
- | <a href="#C"><strong>C</strong></a>
- | <a href="#D"><strong>D</strong></a>
- | <a href="#E"><strong>E</strong></a>
- | <a href="#F"><strong>F</strong></a>
- | <a href="#G"><strong>G</strong></a>
- | <a href="#H"><strong>H</strong></a>
- | <a href="#I"><strong>I</strong></a>
- | <a href="#K"><strong>K</strong></a>
- | <a href="#L"><strong>L</strong></a>
- | <a href="#M"><strong>M</strong></a>
- | <a href="#N"><strong>N</strong></a>
- | <a href="#O"><strong>O</strong></a>
- | <a href="#P"><strong>P</strong></a>
- | <a href="#Q"><strong>Q</strong></a>
- | <a href="#R"><strong>R</strong></a>
- | <a href="#S"><strong>S</strong></a>
- | <a href="#T"><strong>T</strong></a>
- | <a href="#U"><strong>U</strong></a>
- | <a href="#V"><strong>V</strong></a>
- | <a href="#W"><strong>W</strong></a>
- | <a href="#X"><strong>X</strong></a>
- | <a href="#Y"><strong>Y</strong></a>
- | <a href="#Z"><strong>Z</strong></a>
-
-</div>
-<h2 id="A">A</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#HHGate.A">A (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.A">[1]</a>, <a href="moose_classes.html#HHGate.A">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate2D.A">(HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.A">[1]</a>, <a href="moose_classes.html#HHGate2D.A">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IzhikevichNrn.a">a (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.a">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.a">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.abs_refract">abs_refract (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.abs_refract">[1]</a>, <a href="moose_classes.html#SpikeGen.abs_refract">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.absoluteAccuracy">absoluteAccuracy (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.absoluteAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.absoluteAccuracy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.accommodating">accommodating (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.accommodating">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.accommodating">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.activation">activation() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.activation">[1]</a>, <a href="moose_classes.html#SynChan.activation">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor">Adaptor (built-in class)</a>, <a href="moose_builtins.html#Adaptor">[1]</a>, <a href="moose_classes.html#Adaptor">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Shell.addMsg">addMsg() (Shell method)</a>, <a href="moose_builtins.html#Shell.addMsg">[1]</a>, <a href="moose_classes.html#Shell.addMsg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Synapse.addSpike">addSpike() (Synapse method)</a>, <a href="moose_builtins.html#Synapse.addSpike">[1]</a>, <a href="moose_classes.html#Synapse.addSpike">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.aDest">aDest() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.aDest">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.aDest">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.adjacent">adjacent (Msg attribute)</a>, <a href="moose_builtins.html#Msg.adjacent">[1]</a>, <a href="moose_classes.html#Msg.adjacent">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.alpha">alpha (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.alpha">[1]</a>, <a href="moose_classes.html#HHGate.alpha">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.alpha">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.alpha">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.alpha">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.alphaParms">alphaParms (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.alphaParms">[1]</a>, <a href="moose_classes.html#HHGate.alphaParms">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#CubeMesh.alwaysDiffuse">alwaysDiffuse (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.alwaysDiffuse">[1]</a>, <a href="moose_classes.html#CubeMesh.alwaysDiffuse">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator">Annotator (built-in class)</a>, <a href="moose_builtins.html#Annotator">[1]</a>, <a href="moose_classes.html#Annotator">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.anyValue">anyValue (Arith attribute)</a>, <a href="moose_builtins.html#Arith.anyValue">[1]</a>, <a href="moose_classes.html#Arith.anyValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.arg1">arg1() (Arith method)</a>, <a href="moose_builtins.html#Arith.arg1">[1]</a>, <a href="moose_classes.html#Arith.arg1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MathFunc.arg1">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.arg1">[1]</a>, <a href="moose_classes.html#MathFunc.arg1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Arith.arg1Value">arg1Value (Arith attribute)</a>, <a href="moose_builtins.html#Arith.arg1Value">[1]</a>, <a href="moose_classes.html#Arith.arg1Value">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.arg1x2">arg1x2() (Arith method)</a>, <a href="moose_builtins.html#Arith.arg1x2">[1]</a>, <a href="moose_classes.html#Arith.arg1x2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.arg2">arg2() (Arith method)</a>, <a href="moose_builtins.html#Arith.arg2">[1]</a>, <a href="moose_classes.html#Arith.arg2">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MathFunc.arg2">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.arg2">[1]</a>, <a href="moose_classes.html#MathFunc.arg2">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Arith.arg3">arg3() (Arith method)</a>, <a href="moose_builtins.html#Arith.arg3">[1]</a>, <a href="moose_classes.html#Arith.arg3">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MathFunc.arg3">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.arg3">[1]</a>, <a href="moose_classes.html#MathFunc.arg3">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MathFunc.arg4">arg4() (MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.arg4">[1]</a>, <a href="moose_classes.html#MathFunc.arg4">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith">Arith (built-in class)</a>, <a href="moose_builtins.html#Arith">[1]</a>, <a href="moose_classes.html#Arith">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.axial">axial (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.axial">[1]</a>, <a href="moose_classes.html#CompartmentBase.axial">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.axialOut">axialOut (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.axialOut">[1]</a>, <a href="moose_classes.html#CompartmentBase.axialOut">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="B">B</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#CaConc.B">B (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.B">[1]</a>, <a href="moose_classes.html#CaConc.B">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate.B">(HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.B">[1]</a>, <a href="moose_classes.html#HHGate.B">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.B">(HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.B">[1]</a>, <a href="moose_classes.html#HHGate2D.B">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IzhikevichNrn.b">b (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.b">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.b">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCaConc.B">B (ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.B">[1]</a>, <a href="moose_classes.html#ZombieCaConc.B">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.badStoichiometry">badStoichiometry (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.badStoichiometry">[1]</a>, <a href="moose_classes.html#SteadyState.badStoichiometry">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.basal">basal() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.basal">[1]</a>, <a href="moose_classes.html#CaConc.basal">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.basal">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.basal">[1]</a>, <a href="moose_classes.html#ZombieCaConc.basal">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Cinfo.baseClass">baseClass (Cinfo attribute)</a>, <a href="moose_builtins.html#Cinfo.baseClass">[1]</a>, <a href="moose_classes.html#Cinfo.baseClass">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.baseLevel">baseLevel (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.baseLevel">[1]</a>, <a href="moose_classes.html#PulseGen.baseLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.bDest">bDest() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.bDest">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.bDest">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#HHGate.beta">beta (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.beta">[1]</a>, <a href="moose_classes.html#HHGate.beta">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.beta">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.beta">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.beta">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#DifShell.buffer">buffer (DifShell attribute)</a>, <a href="moose_builtins.html#DifShell.buffer">[1]</a>, <a href="moose_classes.html#DifShell.buffer">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PostMaster.bufferSize">bufferSize (PostMaster attribute)</a>, <a href="moose_builtins.html#PostMaster.bufferSize">[1]</a>, <a href="moose_classes.html#PostMaster.bufferSize">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.bufferTime">bufferTime (IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.bufferTime">[1]</a>, <a href="moose_classes.html#IntFire.bufferTime">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.bufferTime">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.bufferTime">[1]</a>, <a href="moose_classes.html#SynChanBase.bufferTime">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#BufPool">BufPool (built-in class)</a>, <a href="moose_builtins.html#BufPool">[1]</a>, <a href="moose_classes.html#BufPool">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChemCompt.buildDefaultMesh">buildDefaultMesh() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.buildDefaultMesh">[1]</a>, <a href="moose_classes.html#ChemCompt.buildDefaultMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.buildNeuroMeshJunctions">buildNeuroMeshJunctions() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.buildNeuroMeshJunctions">[1]</a>, <a href="moose_classes.html#Dsolve.buildNeuroMeshJunctions">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="C">C</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#C">C</a>, <a href="moose_builtins.html#C">[1]</a>, <a href="moose_classes.html#C">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.c">c (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.c">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.c">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.C">C (RC attribute)</a>, <a href="moose_builtins.html#RC.C">[1]</a>, <a href="moose_classes.html#RC.C">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.Ca">Ca (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.Ca">[1]</a>, <a href="moose_classes.html#CaConc.Ca">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.Ca">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.Ca">[1]</a>, <a href="moose_classes.html#ZombieCaConc.Ca">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CaConc.Ca_base">Ca_base (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.Ca_base">[1]</a>, <a href="moose_classes.html#CaConc.Ca_base">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.Ca_base">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.Ca_base">[1]</a>, <a href="moose_classes.html#ZombieCaConc.Ca_base">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HSolve.caAdvance">caAdvance (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.caAdvance">[1]</a>, <a href="moose_classes.html#HSolve.caAdvance">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.CaBasal">CaBasal (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.CaBasal">[1]</a>, <a href="moose_classes.html#CaConc.CaBasal">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.CaBasal">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.CaBasal">[1]</a>, <a href="moose_classes.html#ZombieCaConc.CaBasal">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.cable">cable() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.cable">[1]</a>, <a href="moose_classes.html#CompartmentBase.cable">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc">CaConc (built-in class)</a>, <a href="moose_builtins.html#CaConc">[1]</a>, <a href="moose_classes.html#CaConc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.caDiv">caDiv (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.caDiv">[1]</a>, <a href="moose_classes.html#HSolve.caDiv">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.caMax">caMax (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.caMax">[1]</a>, <a href="moose_classes.html#HSolve.caMax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.caMin">caMin (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.caMin">[1]</a>, <a href="moose_classes.html#HSolve.caMin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.cDest">cDest() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.cDest">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.cDest">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.ceiling">ceiling (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.ceiling">[1]</a>, <a href="moose_classes.html#CaConc.ceiling">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.ceiling">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.ceiling">[1]</a>, <a href="moose_classes.html#ZombieCaConc.ceiling">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.cell">cell (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.cell">[1]</a>, <a href="moose_classes.html#NeuroMesh.cell">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh.cellPortion">cellPortion() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.cellPortion">[1]</a>, <a href="moose_classes.html#NeuroMesh.cellPortion">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ceq">Ceq</a>, <a href="moose_builtins.html#Ceq">[1]</a>, <a href="moose_classes.html#Ceq">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase">ChanBase (built-in class)</a>, <a href="moose_builtins.html#ChanBase">[1]</a>, <a href="moose_classes.html#ChanBase">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.channel">channel (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.channel">[1]</a>, <a href="moose_classes.html#ChanBase.channel">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.channel">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.channel">[1]</a>, <a href="moose_classes.html#CompartmentBase.channel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.channel">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.channel">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.channel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.channel">(MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.channel">[1]</a>, <a href="moose_classes.html#MarkovRateTable.channel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.channel">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.channel">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.channel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.channel">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.channel">[1]</a>, <a href="moose_classes.html#SynChanBase.channel">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#GapJunction.channel1">channel1 (GapJunction attribute)</a>, <a href="moose_builtins.html#GapJunction.channel1">[1]</a>, <a href="moose_classes.html#GapJunction.channel1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#channel1Out">channel1Out</a>, <a href="moose_builtins.html#channel1Out">[1]</a>, <a href="moose_classes.html#channel1Out">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#channel2">channel2</a>, <a href="moose_builtins.html#channel2">[1]</a>, <a href="moose_classes.html#channel2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#channel2Out">channel2Out</a>, <a href="moose_builtins.html#channel2Out">[1]</a>, <a href="moose_classes.html#channel2Out">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.channelOut">channelOut (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.channelOut">[1]</a>, <a href="moose_classes.html#ChanBase.channelOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.channelOut">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.channelOut">[1]</a>, <a href="moose_classes.html#SynChanBase.channelOut">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChemCompt">ChemCompt (built-in class)</a>, <a href="moose_builtins.html#ChemCompt">[1]</a>, <a href="moose_classes.html#ChemCompt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.childOut">childOut (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.childOut">[1]</a>, <a href="moose_classes.html#Neutral.childOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.children">children (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.children">[1]</a>, <a href="moose_classes.html#Neutral.children">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.ci">ci() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.ci">[1]</a>, <a href="moose_classes.html#Nernst.ci">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.Cin">Cin (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.Cin">[1]</a>, <a href="moose_classes.html#Nernst.Cin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Cinfo">Cinfo (built-in class)</a>, <a href="moose_builtins.html#Cinfo">[1]</a>, <a href="moose_classes.html#Cinfo">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.className">className (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.className">[1]</a>, <a href="moose_classes.html#Neutral.className">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.clear">clear() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.clear">[1]</a>, <a href="moose_classes.html#SparseMsg.clear">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.clearVec">clearVec() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.clearVec">[1]</a>, <a href="moose_classes.html#TableBase.clearVec">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock">Clock (built-in class)</a>, <a href="moose_builtins.html#Clock">[1]</a>, <a href="moose_classes.html#Clock">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.clockControl">clockControl (Clock attribute)</a>, <a href="moose_builtins.html#Clock.clockControl">[1]</a>, <a href="moose_classes.html#Clock.clockControl">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.Cm">Cm (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Cm">[1]</a>, <a href="moose_classes.html#CompartmentBase.Cm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.CMg">CMg (MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.CMg">[1]</a>, <a href="moose_classes.html#MgBlock.CMg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.co">co() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.co">[1]</a>, <a href="moose_classes.html#Nernst.co">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Annotator.color">color (Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.color">[1]</a>, <a href="moose_classes.html#Annotator.color">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.columnIndex">columnIndex (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.columnIndex">[1]</a>, <a href="moose_classes.html#Stoich.columnIndex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.command">command (PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.command">[1]</a>, <a href="moose_classes.html#PIDController.command">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VClamp.command">(VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.command">[1]</a>, <a href="moose_classes.html#VClamp.command">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PIDController.commandIn">commandIn() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.commandIn">[1]</a>, <a href="moose_classes.html#PIDController.commandIn">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VClamp.commandIn">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.commandIn">[1]</a>, <a href="moose_classes.html#VClamp.commandIn">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#TableBase.compareVec">compareVec() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.compareVec">[1]</a>, <a href="moose_classes.html#TableBase.compareVec">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.compareXplot">compareXplot() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.compareXplot">[1]</a>, <a href="moose_classes.html#TableBase.compareXplot">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Compartment">Compartment (built-in class)</a>, <a href="moose_builtins.html#Compartment">[1]</a>, <a href="moose_classes.html#Compartment">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.compartment">compartment (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.compartment">[1]</a>, <a href="moose_classes.html#Dsolve.compartment">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Ksolve.compartment">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.compartment">[1]</a>, <a href="moose_classes.html#Ksolve.compartment">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.compartment">(Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.compartment">[1]</a>, <a href="moose_classes.html#Stoich.compartment">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase">CompartmentBase (built-in class)</a>, <a href="moose_builtins.html#CompartmentBase">[1]</a>, <a href="moose_classes.html#CompartmentBase">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.conc">conc (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.conc">[1]</a>, <a href="moose_classes.html#PoolBase.conc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.concen">concen() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.concen">[1]</a>, <a href="moose_classes.html#HHChannel.concen">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.concen">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.concen">[1]</a>, <a href="moose_classes.html#HHChannel2D.concen">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.concen">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.concen">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.concen">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel2D.concen2">concen2() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.concen2">[1]</a>, <a href="moose_classes.html#HHChannel2D.concen2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#concentrationOut">concentrationOut</a>, <a href="moose_builtins.html#concentrationOut">[1]</a>, <a href="moose_classes.html#concentrationOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.concInit">concInit (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.concInit">[1]</a>, <a href="moose_classes.html#PoolBase.concInit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.concK1">concK1 (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.concK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.concK1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.concOut">concOut (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.concOut">[1]</a>, <a href="moose_classes.html#CaConc.concOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.concOut">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.concOut">[1]</a>, <a href="moose_classes.html#ZombieCaConc.concOut">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SteadyState.convergenceCriterion">convergenceCriterion (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.convergenceCriterion">[1]</a>, <a href="moose_classes.html#SteadyState.convergenceCriterion">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.Coordinates">Coordinates (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.Coordinates">[1]</a>, <a href="moose_classes.html#MeshEntry.Coordinates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.coords">coords (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.coords">[1]</a>, <a href="moose_classes.html#CubeMesh.coords">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.coords">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.coords">[1]</a>, <a href="moose_classes.html#CylMesh.coords">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Shell.copy">copy() (Shell method)</a>, <a href="moose_builtins.html#Shell.copy">[1]</a>, <a href="moose_classes.html#Shell.copy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.count">count (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.count">[1]</a>, <a href="moose_classes.html#PulseGen.count">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.Cout">Cout (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.Cout">[1]</a>, <a href="moose_classes.html#Nernst.Cout">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.cplx">cplx (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.cplx">[1]</a>, <a href="moose_classes.html#CplxEnzBase.cplx">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.cplxDest">cplxDest() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.cplxDest">[1]</a>, <a href="moose_classes.html#CplxEnzBase.cplxDest">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase">CplxEnzBase (built-in class)</a>, <a href="moose_builtins.html#CplxEnzBase">[1]</a>, <a href="moose_classes.html#CplxEnzBase">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.cplxOut">cplxOut (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.cplxOut">[1]</a>, <a href="moose_classes.html#CplxEnzBase.cplxOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Shell.create">create() (Shell method)</a>, <a href="moose_builtins.html#Shell.create">[1]</a>, <a href="moose_classes.html#Shell.create">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.createGate">createGate() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.createGate">[1]</a>, <a href="moose_classes.html#HHChannel.createGate">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieHHChannel.createGate">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.createGate">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.createGate">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh">CubeMesh (built-in class)</a>, <a href="moose_builtins.html#CubeMesh">[1]</a>, <a href="moose_classes.html#CubeMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.current">current (VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.current">[1]</a>, <a href="moose_classes.html#VClamp.current">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.current">current() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.current">[1]</a>, <a href="moose_classes.html#CaConc.current">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.current">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.current">[1]</a>, <a href="moose_classes.html#ZombieCaConc.current">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CaConc.currentFraction">currentFraction() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.currentFraction">[1]</a>, <a href="moose_classes.html#CaConc.currentFraction">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.currentFraction">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.currentFraction">[1]</a>, <a href="moose_classes.html#ZombieCaConc.currentFraction">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#VClamp.currentOut">currentOut (VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.currentOut">[1]</a>, <a href="moose_classes.html#VClamp.currentOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.currentStep">currentStep (Clock attribute)</a>, <a href="moose_builtins.html#Clock.currentStep">[1]</a>, <a href="moose_classes.html#Clock.currentStep">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.currentTime">currentTime (Clock attribute)</a>, <a href="moose_builtins.html#Clock.currentTime">[1]</a>, <a href="moose_classes.html#Clock.currentTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#cylinder">cylinder</a>, <a href="moose_builtins.html#cylinder">[1]</a>, <a href="moose_classes.html#cylinder">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#cylinderOut">cylinderOut</a>, <a href="moose_builtins.html#cylinderOut">[1]</a>, <a href="moose_classes.html#cylinderOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh">CylMesh (built-in class)</a>, <a href="moose_builtins.html#CylMesh">[1]</a>, <a href="moose_classes.html#CylMesh">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="D">D</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#D">D</a>, <a href="moose_builtins.html#D">[1]</a>, <a href="moose_classes.html#D">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.d">d (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.d">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.d">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.dDest">dDest() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.dDest">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.dDest">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.decrease">decrease() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.decrease">[1]</a>, <a href="moose_classes.html#CaConc.decrease">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.decrease">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.decrease">[1]</a>, <a href="moose_classes.html#ZombieCaConc.decrease">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Pool.decrement">decrement() (Pool method)</a>, <a href="moose_builtins.html#Pool.decrement">[1]</a>, <a href="moose_classes.html#Pool.decrement">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.delay">delay (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.delay">[1]</a>, <a href="moose_classes.html#PulseGen.delay">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Synapse.delay">(Synapse attribute)</a>, <a href="moose_builtins.html#Synapse.delay">[1]</a>, <a href="moose_classes.html#Synapse.delay">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.delayIn">delayIn() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.delayIn">[1]</a>, <a href="moose_classes.html#PulseGen.delayIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Shell.delete">delete() (Shell method)</a>, <a href="moose_builtins.html#Shell.delete">[1]</a>, <a href="moose_classes.html#Shell.delete">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#derivative">derivative</a>, <a href="tmp.html#derivative">[1]</a>, <a href="moose_builtins.html#derivative">[2]</a>, <a href="moose_builtins.html#derivative">[3]</a>, <a href="moose_classes.html#derivative">[4]</a>, <a href="moose_classes.html#derivative">[5]</a>
- </dt>
-
-
- <dt><a href="tmp.html#derivativeOut">derivativeOut</a>, <a href="moose_builtins.html#derivativeOut">[1]</a>, <a href="moose_classes.html#derivativeOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Finfo.dest">dest (Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.dest">[1]</a>, <a href="moose_classes.html#Finfo.dest">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.destFields">destFields (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.destFields">[1]</a>, <a href="moose_classes.html#Neutral.destFields">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.destFieldsOnE1">destFieldsOnE1 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.destFieldsOnE1">[1]</a>, <a href="moose_classes.html#Msg.destFieldsOnE1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.destFieldsOnE2">destFieldsOnE2 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.destFieldsOnE2">[1]</a>, <a href="moose_classes.html#Msg.destFieldsOnE2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiagonalMsg">DiagonalMsg (built-in class)</a>, <a href="moose_builtins.html#DiagonalMsg">[1]</a>, <a href="moose_classes.html#DiagonalMsg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#diameter">diameter</a>, <a href="moose_builtins.html#diameter">[1]</a>, <a href="moose_classes.html#diameter">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.diameter">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.diameter">[1]</a>, <a href="moose_classes.html#CompartmentBase.diameter">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#DiffAmp">DiffAmp (built-in class)</a>, <a href="moose_builtins.html#DiffAmp">[1]</a>, <a href="moose_classes.html#DiffAmp">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.diffConst">diffConst (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.diffConst">[1]</a>, <a href="moose_classes.html#PoolBase.diffConst">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#CylMesh.diffLength">diffLength (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.diffLength">[1]</a>, <a href="moose_classes.html#CylMesh.diffLength">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#NeuroMesh.diffLength">(NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.diffLength">[1]</a>, <a href="moose_classes.html#NeuroMesh.diffLength">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MeshEntry.DiffusionArea">DiffusionArea (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.DiffusionArea">[1]</a>, <a href="moose_classes.html#MeshEntry.DiffusionArea">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.DiffusionScaling">DiffusionScaling (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.DiffusionScaling">[1]</a>, <a href="moose_classes.html#MeshEntry.DiffusionScaling">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DifShell">DifShell (built-in class)</a>, <a href="moose_builtins.html#DifShell">[1]</a>, <a href="moose_classes.html#DifShell">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.dimensions">dimensions (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.dimensions">[1]</a>, <a href="moose_classes.html#MeshEntry.dimensions">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#distal">distal</a>, <a href="moose_builtins.html#distal">[1]</a>, <a href="moose_classes.html#distal">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#distalOut">distalOut</a>, <a href="tmp.html#distalOut">[1]</a>, <a href="tmp.html#distalOut">[2]</a>, <a href="moose_builtins.html#distalOut">[3]</a>, <a href="moose_builtins.html#distalOut">[4]</a>, <a href="moose_builtins.html#distalOut">[5]</a>, <a href="moose_classes.html#distalOut">[6]</a>, <a href="moose_classes.html#distalOut">[7]</a>, <a href="moose_classes.html#distalOut">[8]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.divs">divs (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.divs">[1]</a>, <a href="moose_classes.html#HHGate.divs">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Cinfo.docs">docs (Cinfo attribute)</a>, <a href="moose_builtins.html#Cinfo.docs">[1]</a>, <a href="moose_classes.html#Cinfo.docs">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Finfo.docs">(Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.docs">[1]</a>, <a href="moose_classes.html#Finfo.docs">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#StimulusTable.doLoop">doLoop (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.doLoop">[1]</a>, <a href="moose_classes.html#StimulusTable.doLoop">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Double">Double (built-in class)</a>, <a href="moose_builtins.html#Double">[1]</a>, <a href="moose_classes.html#Double">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve">Dsolve (built-in class)</a>, <a href="moose_builtins.html#Dsolve">[1]</a>, <a href="moose_classes.html#Dsolve">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.dsolve">dsolve (Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.dsolve">[1]</a>, <a href="moose_classes.html#Ksolve.dsolve">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Stoich.dsolve">(Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.dsolve">[1]</a>, <a href="moose_classes.html#Stoich.dsolve">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.dt">dt (Clock attribute)</a>, <a href="moose_builtins.html#Clock.dt">[1]</a>, <a href="moose_classes.html#Clock.dt">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HSolve.dt">(HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.dt">[1]</a>, <a href="moose_classes.html#HSolve.dt">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.dts">dts (Clock attribute)</a>, <a href="moose_builtins.html#Clock.dts">[1]</a>, <a href="moose_classes.html#Clock.dts">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.dx">dx (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.dx">[1]</a>, <a href="moose_classes.html#CubeMesh.dx">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.dx">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.dx">[1]</a>, <a href="moose_classes.html#Interpol2D.dx">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.dy">dy (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.dy">[1]</a>, <a href="moose_classes.html#CubeMesh.dy">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.dy">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.dy">[1]</a>, <a href="moose_classes.html#Interpol2D.dy">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.dz">dz (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.dz">[1]</a>, <a href="moose_classes.html#CubeMesh.dz">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="E">E</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Nernst.E">E (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.E">[1]</a>, <a href="moose_classes.html#Nernst.E">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.e1">e1 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.e1">[1]</a>, <a href="moose_classes.html#Msg.e1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.e2">e2 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.e2">[1]</a>, <a href="moose_classes.html#Msg.e2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#e_previous">e_previous</a>, <a href="moose_builtins.html#e_previous">[1]</a>, <a href="moose_classes.html#e_previous">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.edgeTriggered">edgeTriggered (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.edgeTriggered">[1]</a>, <a href="moose_classes.html#SpikeGen.edgeTriggered">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.eigenvalues">eigenvalues (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.eigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.eigenvalues">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.Ek">Ek (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.Ek">[1]</a>, <a href="moose_classes.html#ChanBase.Ek">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.Ek">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.Ek">[1]</a>, <a href="moose_classes.html#SynChanBase.Ek">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.Ek">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Ek">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Ek">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.Em">Em (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Em">[1]</a>, <a href="moose_classes.html#CompartmentBase.Em">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Enz">Enz (built-in class)</a>, <a href="moose_builtins.html#Enz">[1]</a>, <a href="moose_classes.html#Enz">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.enz">enz (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.enz">[1]</a>, <a href="moose_classes.html#CplxEnzBase.enz">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase">EnzBase (built-in class)</a>, <a href="moose_builtins.html#EnzBase">[1]</a>, <a href="moose_classes.html#EnzBase">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#CplxEnzBase.enzDest">enzDest() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.enzDest">[1]</a>, <a href="moose_classes.html#CplxEnzBase.enzDest">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#EnzBase.enzDest">(EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.enzDest">[1]</a>, <a href="moose_classes.html#EnzBase.enzDest">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CplxEnzBase.enzOut">enzOut (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.enzOut">[1]</a>, <a href="moose_classes.html#CplxEnzBase.enzOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.Eout">Eout (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.Eout">[1]</a>, <a href="moose_classes.html#Nernst.Eout">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.epsAbs">epsAbs (Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.epsAbs">[1]</a>, <a href="moose_classes.html#Ksolve.epsAbs">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.epsRel">epsRel (Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.epsRel">[1]</a>, <a href="moose_classes.html#Ksolve.epsRel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#eqTauPump">eqTauPump()</a>, <a href="moose_builtins.html#eqTauPump">[1]</a>, <a href="moose_classes.html#eqTauPump">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#error">error</a>, <a href="moose_builtins.html#error">[1]</a>, <a href="moose_classes.html#error">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.estimatedDt">estimatedDt (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.estimatedDt">[1]</a>, <a href="moose_classes.html#Stoich.estimatedDt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.eventOut">eventOut (TimeTable attribute)</a>, <a href="moose_builtins.html#TimeTable.eventOut">[1]</a>, <a href="moose_classes.html#TimeTable.eventOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#expr">expr</a>, <a href="moose_builtins.html#expr">[1]</a>, <a href="moose_classes.html#expr">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="F">F</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Finfo.fieldName">fieldName (Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.fieldName">[1]</a>, <a href="moose_classes.html#Finfo.fieldName">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.filename">filename (TimeTable attribute)</a>, <a href="moose_builtins.html#TimeTable.filename">[1]</a>, <a href="moose_classes.html#TimeTable.filename">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#fInflux">fInflux()</a>, <a href="moose_builtins.html#fInflux">[1]</a>, <a href="moose_classes.html#fInflux">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Finfo">Finfo (built-in class)</a>, <a href="moose_builtins.html#Finfo">[1]</a>, <a href="moose_classes.html#Finfo">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.finished">finished (Clock attribute)</a>, <a href="moose_builtins.html#Clock.finished">[1]</a>, <a href="moose_classes.html#Clock.finished">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.firstDelay">firstDelay (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.firstDelay">[1]</a>, <a href="moose_classes.html#PulseGen.firstDelay">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.firstLevel">firstLevel (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.firstLevel">[1]</a>, <a href="moose_classes.html#PulseGen.firstLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.firstWidth">firstWidth (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.firstWidth">[1]</a>, <a href="moose_classes.html#PulseGen.firstWidth">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#CaConc.floor">floor (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.floor">[1]</a>, <a href="moose_classes.html#CaConc.floor">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.floor">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.floor">[1]</a>, <a href="moose_classes.html#ZombieCaConc.floor">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#fluxFromIn">fluxFromIn()</a>, <a href="moose_builtins.html#fluxFromIn">[1]</a>, <a href="moose_classes.html#fluxFromIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#fluxFromOut">fluxFromOut()</a>, <a href="moose_builtins.html#fluxFromOut">[1]</a>, <a href="moose_classes.html#fluxFromOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#fOutflux">fOutflux()</a>, <a href="moose_builtins.html#fOutflux">[1]</a>, <a href="moose_classes.html#fOutflux">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func">Func (built-in class)</a>, <a href="moose_builtins.html#Func">[1]</a>, <a href="moose_classes.html#Func">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#FuncBase">FuncBase (built-in class)</a>, <a href="moose_builtins.html#FuncBase">[1]</a>, <a href="moose_classes.html#FuncBase">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#FuncPool">FuncPool (built-in class)</a>, <a href="moose_builtins.html#FuncPool">[1]</a>, <a href="moose_classes.html#FuncPool">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.function">function (Arith attribute)</a>, <a href="moose_builtins.html#Arith.function">[1]</a>, <a href="moose_classes.html#Arith.function">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MathFunc.function">(MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.function">[1]</a>, <a href="moose_classes.html#MathFunc.function">[2]</a>
- </dt>
-
- </dl></dd>
- </dl></td>
-</tr></table>
-
-<h2 id="G">G</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#gain">gain</a>, <a href="moose_builtins.html#gain">[1]</a>, <a href="moose_classes.html#gain">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#DiffAmp.gain">(DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.gain">[1]</a>, <a href="moose_classes.html#DiffAmp.gain">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.gain">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.gain">[1]</a>, <a href="moose_classes.html#PIDController.gain">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PIDController.gainDest">gainDest() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.gainDest">[1]</a>, <a href="moose_classes.html#PIDController.gainDest">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.gainIn">gainIn() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.gainIn">[1]</a>, <a href="moose_classes.html#DiffAmp.gainIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.gamma">gamma (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.gamma">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.gamma">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#GapJunction">GapJunction (built-in class)</a>, <a href="moose_builtins.html#GapJunction">[1]</a>, <a href="moose_classes.html#GapJunction">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.Gbar">Gbar (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.Gbar">[1]</a>, <a href="moose_classes.html#ChanBase.Gbar">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.gbar">gbar (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.gbar">[1]</a>, <a href="moose_classes.html#MarkovChannel.gbar">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.Gbar">Gbar (SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.Gbar">[1]</a>, <a href="moose_classes.html#SynChanBase.Gbar">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieHHChannel.Gbar">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Gbar">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Gbar">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.geometryPolicy">geometryPolicy (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.geometryPolicy">[1]</a>, <a href="moose_classes.html#NeuroMesh.geometryPolicy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.getA">getA() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getA">[1]</a>, <a href="moose_classes.html#HHGate.getA">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate2D.getA">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getA">[1]</a>, <a href="moose_classes.html#HHGate2D.getA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.getA">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getA">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getA">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SpikeGen.getAbs_refract">getAbs_refract() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getAbs_refract">[1]</a>, <a href="moose_classes.html#SpikeGen.getAbs_refract">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.getAbsoluteAccuracy">getAbsoluteAccuracy() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getAbsoluteAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getAbsoluteAccuracy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.getAccommodating">getAccommodating() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getAccommodating">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getAccommodating">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.getAdjacent">getAdjacent() (Msg method)</a>, <a href="moose_builtins.html#Msg.getAdjacent">[1]</a>, <a href="moose_classes.html#Msg.getAdjacent">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.getAlpha">getAlpha() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getAlpha">[1]</a>, <a href="moose_classes.html#HHGate.getAlpha">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.getAlpha">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getAlpha">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getAlpha">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.getAlphaParms">getAlphaParms() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getAlphaParms">[1]</a>, <a href="moose_classes.html#HHGate.getAlphaParms">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getAlwaysDiffuse">getAlwaysDiffuse() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getAlwaysDiffuse">[1]</a>, <a href="moose_classes.html#CubeMesh.getAlwaysDiffuse">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.getAnyValue">getAnyValue() (Arith method)</a>, <a href="moose_builtins.html#Arith.getAnyValue">[1]</a>, <a href="moose_classes.html#Arith.getAnyValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.getArg1Value">getArg1Value() (Arith method)</a>, <a href="moose_builtins.html#Arith.getArg1Value">[1]</a>, <a href="moose_classes.html#Arith.getArg1Value">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.getB">getB() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getB">[1]</a>, <a href="moose_classes.html#CaConc.getB">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate.getB">(HHGate method)</a>, <a href="moose_builtins.html#HHGate.getB">[1]</a>, <a href="moose_classes.html#HHGate.getB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.getB">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getB">[1]</a>, <a href="moose_classes.html#HHGate2D.getB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.getB">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getB">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCaConc.getB">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getB">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getB">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SteadyState.getBadStoichiometry">getBadStoichiometry() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getBadStoichiometry">[1]</a>, <a href="moose_classes.html#SteadyState.getBadStoichiometry">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Cinfo.getBaseClass">getBaseClass() (Cinfo method)</a>, <a href="moose_builtins.html#Cinfo.getBaseClass">[1]</a>, <a href="moose_classes.html#Cinfo.getBaseClass">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getBaseLevel">getBaseLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getBaseLevel">[1]</a>, <a href="moose_classes.html#PulseGen.getBaseLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.getBeta">getBeta() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getBeta">[1]</a>, <a href="moose_classes.html#HHGate.getBeta">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.getBeta">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getBeta">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getBeta">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PostMaster.getBufferSize">getBufferSize() (PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.getBufferSize">[1]</a>, <a href="moose_classes.html#PostMaster.getBufferSize">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.getBufferTime">getBufferTime() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.getBufferTime">[1]</a>, <a href="moose_classes.html#IntFire.getBufferTime">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.getBufferTime">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getBufferTime">[1]</a>, <a href="moose_classes.html#SynChanBase.getBufferTime">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#getC">getC()</a>, <a href="moose_builtins.html#getC">[1]</a>, <a href="moose_classes.html#getC">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.getC">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getC">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getC">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.getC">(RC method)</a>, <a href="moose_builtins.html#RC.getC">[1]</a>, <a href="moose_classes.html#RC.getC">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CaConc.getCa">getCa() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getCa">[1]</a>, <a href="moose_classes.html#CaConc.getCa">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.getCa">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getCa">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getCa">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CaConc.getCa_base">getCa_base() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getCa_base">[1]</a>, <a href="moose_classes.html#CaConc.getCa_base">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.getCa_base">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getCa_base">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getCa_base">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HSolve.getCaAdvance">getCaAdvance() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getCaAdvance">[1]</a>, <a href="moose_classes.html#HSolve.getCaAdvance">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.getCaBasal">getCaBasal() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getCaBasal">[1]</a>, <a href="moose_classes.html#CaConc.getCaBasal">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.getCaBasal">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getCaBasal">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getCaBasal">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HSolve.getCaDiv">getCaDiv() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getCaDiv">[1]</a>, <a href="moose_classes.html#HSolve.getCaDiv">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.getCaMax">getCaMax() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getCaMax">[1]</a>, <a href="moose_classes.html#HSolve.getCaMax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.getCaMin">getCaMin() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getCaMin">[1]</a>, <a href="moose_classes.html#HSolve.getCaMin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.getCeiling">getCeiling() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getCeiling">[1]</a>, <a href="moose_classes.html#CaConc.getCeiling">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.getCeiling">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getCeiling">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getCeiling">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.getCell">getCell() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getCell">[1]</a>, <a href="moose_classes.html#NeuroMesh.getCell">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getCeq">getCeq()</a>, <a href="moose_builtins.html#getCeq">[1]</a>, <a href="moose_classes.html#getCeq">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getChildren">getChildren() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getChildren">[1]</a>, <a href="moose_classes.html#Neutral.getChildren">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.getCin">getCin() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.getCin">[1]</a>, <a href="moose_classes.html#Nernst.getCin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getClassName">getClassName() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getClassName">[1]</a>, <a href="moose_classes.html#Neutral.getClassName">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.getCm">getCm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getCm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getCm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.getCMg">getCMg() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getCMg">[1]</a>, <a href="moose_classes.html#MgBlock.getCMg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.getColor">getColor() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getColor">[1]</a>, <a href="moose_classes.html#Annotator.getColor">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.getColumnIndex">getColumnIndex() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getColumnIndex">[1]</a>, <a href="moose_classes.html#Stoich.getColumnIndex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.getCommand">getCommand() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getCommand">[1]</a>, <a href="moose_classes.html#PIDController.getCommand">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VClamp.getCommand">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getCommand">[1]</a>, <a href="moose_classes.html#VClamp.getCommand">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Dsolve.getCompartment">getCompartment() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getCompartment">[1]</a>, <a href="moose_classes.html#Dsolve.getCompartment">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Ksolve.getCompartment">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getCompartment">[1]</a>, <a href="moose_classes.html#Ksolve.getCompartment">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.getCompartment">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.getCompartment">[1]</a>, <a href="moose_classes.html#Stoich.getCompartment">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PoolBase.getConc">getConc() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getConc">[1]</a>, <a href="moose_classes.html#PoolBase.getConc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.getConcInit">getConcInit() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getConcInit">[1]</a>, <a href="moose_classes.html#PoolBase.getConcInit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.getConcK1">getConcK1() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getConcK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getConcK1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getConvergenceCriterion">getConvergenceCriterion() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getConvergenceCriterion">[1]</a>, <a href="moose_classes.html#SteadyState.getConvergenceCriterion">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.getCoordinates">getCoordinates() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getCoordinates">[1]</a>, <a href="moose_classes.html#MeshEntry.getCoordinates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getCoords">getCoords() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getCoords">[1]</a>, <a href="moose_classes.html#CubeMesh.getCoords">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.getCoords">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getCoords">[1]</a>, <a href="moose_classes.html#CylMesh.getCoords">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.getCount">getCount() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getCount">[1]</a>, <a href="moose_classes.html#PulseGen.getCount">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.getCout">getCout() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.getCout">[1]</a>, <a href="moose_classes.html#Nernst.getCout">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.getCurrent">getCurrent() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.getCurrent">[1]</a>, <a href="moose_classes.html#VClamp.getCurrent">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.getCurrentStep">getCurrentStep() (Clock method)</a>, <a href="moose_builtins.html#Clock.getCurrentStep">[1]</a>, <a href="moose_classes.html#Clock.getCurrentStep">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.getCurrentTime">getCurrentTime() (Clock method)</a>, <a href="moose_builtins.html#Clock.getCurrentTime">[1]</a>, <a href="moose_classes.html#Clock.getCurrentTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getD">getD()</a>, <a href="moose_builtins.html#getD">[1]</a>, <a href="moose_classes.html#getD">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.getD">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getD">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getD">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.getDelay">getDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getDelay">[1]</a>, <a href="moose_classes.html#PulseGen.getDelay">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Synapse.getDelay">(Synapse method)</a>, <a href="moose_builtins.html#Synapse.getDelay">[1]</a>, <a href="moose_classes.html#Synapse.getDelay">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Func.getDerivative">getDerivative() (Func method)</a>, <a href="moose_builtins.html#Func.getDerivative">[1]</a>, <a href="moose_classes.html#Func.getDerivative">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#PIDController.getDerivative">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.getDerivative">[1]</a>, <a href="moose_classes.html#PIDController.getDerivative">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Finfo.getDest">getDest() (Finfo method)</a>, <a href="moose_builtins.html#Finfo.getDest">[1]</a>, <a href="moose_classes.html#Finfo.getDest">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getDestFields">getDestFields() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getDestFields">[1]</a>, <a href="moose_classes.html#Neutral.getDestFields">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.getDestFieldsOnE1">getDestFieldsOnE1() (Msg method)</a>, <a href="moose_builtins.html#Msg.getDestFieldsOnE1">[1]</a>, <a href="moose_classes.html#Msg.getDestFieldsOnE1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.getDestFieldsOnE2">getDestFieldsOnE2() (Msg method)</a>, <a href="moose_builtins.html#Msg.getDestFieldsOnE2">[1]</a>, <a href="moose_classes.html#Msg.getDestFieldsOnE2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getDiameter">getDiameter()</a>, <a href="moose_builtins.html#getDiameter">[1]</a>, <a href="moose_classes.html#getDiameter">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.getDiameter">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getDiameter">[1]</a>, <a href="moose_classes.html#CompartmentBase.getDiameter">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PoolBase.getDiffConst">getDiffConst() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getDiffConst">[1]</a>, <a href="moose_classes.html#PoolBase.getDiffConst">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.getDiffLength">getDiffLength() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getDiffLength">[1]</a>, <a href="moose_classes.html#CylMesh.getDiffLength">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#NeuroMesh.getDiffLength">(NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getDiffLength">[1]</a>, <a href="moose_classes.html#NeuroMesh.getDiffLength">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MeshEntry.getDiffusionArea">getDiffusionArea() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getDiffusionArea">[1]</a>, <a href="moose_classes.html#MeshEntry.getDiffusionArea">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.getDiffusionScaling">getDiffusionScaling() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getDiffusionScaling">[1]</a>, <a href="moose_classes.html#MeshEntry.getDiffusionScaling">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.getDimensions">getDimensions() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getDimensions">[1]</a>, <a href="moose_classes.html#MeshEntry.getDimensions">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.getDivs">getDivs() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getDivs">[1]</a>, <a href="moose_classes.html#HHGate.getDivs">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Cinfo.getDocs">getDocs() (Cinfo method)</a>, <a href="moose_builtins.html#Cinfo.getDocs">[1]</a>, <a href="moose_classes.html#Cinfo.getDocs">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Finfo.getDocs">(Finfo method)</a>, <a href="moose_builtins.html#Finfo.getDocs">[1]</a>, <a href="moose_classes.html#Finfo.getDocs">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#StimulusTable.getDoLoop">getDoLoop() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getDoLoop">[1]</a>, <a href="moose_classes.html#StimulusTable.getDoLoop">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.getDsolve">getDsolve() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getDsolve">[1]</a>, <a href="moose_classes.html#Ksolve.getDsolve">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Stoich.getDsolve">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.getDsolve">[1]</a>, <a href="moose_classes.html#Stoich.getDsolve">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.getDt">getDt() (Clock method)</a>, <a href="moose_builtins.html#Clock.getDt">[1]</a>, <a href="moose_classes.html#Clock.getDt">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HSolve.getDt">(HSolve method)</a>, <a href="moose_builtins.html#HSolve.getDt">[1]</a>, <a href="moose_classes.html#HSolve.getDt">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.getDts">getDts() (Clock method)</a>, <a href="moose_builtins.html#Clock.getDts">[1]</a>, <a href="moose_classes.html#Clock.getDts">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getDx">getDx() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getDx">[1]</a>, <a href="moose_classes.html#CubeMesh.getDx">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.getDx">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getDx">[1]</a>, <a href="moose_classes.html#Interpol2D.getDx">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.getDy">getDy() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getDy">[1]</a>, <a href="moose_classes.html#CubeMesh.getDy">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.getDy">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getDy">[1]</a>, <a href="moose_classes.html#Interpol2D.getDy">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.getDz">getDz() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getDz">[1]</a>, <a href="moose_classes.html#CubeMesh.getDz">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.getE">getE() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.getE">[1]</a>, <a href="moose_classes.html#Nernst.getE">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.getE1">getE1() (Msg method)</a>, <a href="moose_builtins.html#Msg.getE1">[1]</a>, <a href="moose_classes.html#Msg.getE1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.getE2">getE2() (Msg method)</a>, <a href="moose_builtins.html#Msg.getE2">[1]</a>, <a href="moose_classes.html#Msg.getE2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.getE_previous">getE_previous() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getE_previous">[1]</a>, <a href="moose_classes.html#PIDController.getE_previous">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.getEdgeTriggered">getEdgeTriggered() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getEdgeTriggered">[1]</a>, <a href="moose_classes.html#SpikeGen.getEdgeTriggered">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getEigenvalues">getEigenvalues() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.getEigenvalues">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.getEk">getEk() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.getEk">[1]</a>, <a href="moose_classes.html#ChanBase.getEk">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.getEk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getEk">[1]</a>, <a href="moose_classes.html#SynChanBase.getEk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getEk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getEk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getEk">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.getEm">getEm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getEm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getEm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.getEpsAbs">getEpsAbs() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getEpsAbs">[1]</a>, <a href="moose_classes.html#Ksolve.getEpsAbs">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.getEpsRel">getEpsRel() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getEpsRel">[1]</a>, <a href="moose_classes.html#Ksolve.getEpsRel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.getError">getError() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getError">[1]</a>, <a href="moose_classes.html#PIDController.getError">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.getEstimatedDt">getEstimatedDt() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getEstimatedDt">[1]</a>, <a href="moose_classes.html#Stoich.getEstimatedDt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.getExpr">getExpr() (Func method)</a>, <a href="moose_builtins.html#Func.getExpr">[1]</a>, <a href="moose_classes.html#Func.getExpr">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Finfo.getFieldName">getFieldName() (Finfo method)</a>, <a href="moose_builtins.html#Finfo.getFieldName">[1]</a>, <a href="moose_classes.html#Finfo.getFieldName">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.getFilename">getFilename() (TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.getFilename">[1]</a>, <a href="moose_classes.html#TimeTable.getFilename">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getFirstDelay">getFirstDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getFirstDelay">[1]</a>, <a href="moose_classes.html#PulseGen.getFirstDelay">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getFirstLevel">getFirstLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getFirstLevel">[1]</a>, <a href="moose_classes.html#PulseGen.getFirstLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getFirstWidth">getFirstWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getFirstWidth">[1]</a>, <a href="moose_classes.html#PulseGen.getFirstWidth">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.getFloor">getFloor() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getFloor">[1]</a>, <a href="moose_classes.html#CaConc.getFloor">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.getFloor">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getFloor">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getFloor">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Arith.getFunction">getFunction() (Arith method)</a>, <a href="moose_builtins.html#Arith.getFunction">[1]</a>, <a href="moose_classes.html#Arith.getFunction">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MathFunc.getFunction">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.getFunction">[1]</a>, <a href="moose_classes.html#MathFunc.getFunction">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#DiffAmp.getGain">getGain() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.getGain">[1]</a>, <a href="moose_classes.html#DiffAmp.getGain">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#PIDController.getGain">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.getGain">[1]</a>, <a href="moose_classes.html#PIDController.getGain">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.getGain">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getGain">[1]</a>, <a href="moose_classes.html#VClamp.getGain">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IzhikevichNrn.getGamma">getGamma() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getGamma">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getGamma">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.getGbar">getGbar() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.getGbar">[1]</a>, <a href="moose_classes.html#ChanBase.getGbar">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovChannel.getGbar">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getGbar">[1]</a>, <a href="moose_classes.html#MarkovChannel.getGbar">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.getGbar">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getGbar">[1]</a>, <a href="moose_classes.html#SynChanBase.getGbar">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getGbar">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getGbar">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getGbar">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.getGeometryPolicy">getGeometryPolicy() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getGeometryPolicy">[1]</a>, <a href="moose_classes.html#NeuroMesh.getGeometryPolicy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getGk">getGk()</a>, <a href="moose_builtins.html#getGk">[1]</a>, <a href="moose_classes.html#getGk">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ChanBase.getGk">(ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.getGk">[1]</a>, <a href="moose_classes.html#ChanBase.getGk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.getGk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getGk">[1]</a>, <a href="moose_classes.html#SynChanBase.getGk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getGk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getGk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getGk">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SpikeGen.getHasFired">getHasFired() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getHasFired">[1]</a>, <a href="moose_classes.html#SpikeGen.getHasFired">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#OneToAllMsg.getI1">getI1() (OneToAllMsg method)</a>, <a href="moose_builtins.html#OneToAllMsg.getI1">[1]</a>, <a href="moose_classes.html#OneToAllMsg.getI1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SingleMsg.getI1">(SingleMsg method)</a>, <a href="moose_builtins.html#SingleMsg.getI1">[1]</a>, <a href="moose_classes.html#SingleMsg.getI1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SingleMsg.getI2">getI2() (SingleMsg method)</a>, <a href="moose_builtins.html#SingleMsg.getI2">[1]</a>, <a href="moose_classes.html#SingleMsg.getI2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.getIcon">getIcon() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getIcon">[1]</a>, <a href="moose_classes.html#Annotator.getIcon">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.getIk">getIk() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.getIk">[1]</a>, <a href="moose_classes.html#ChanBase.getIk">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MgBlock.getIk">(MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getIk">[1]</a>, <a href="moose_classes.html#MgBlock.getIk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.getIk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.getIk">[1]</a>, <a href="moose_classes.html#SynChanBase.getIk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getIk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getIk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getIk">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.getIm">getIm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getIm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getIm">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.getIm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getIm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getIm">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovChannel.getInitialState">getInitialState() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getInitialState">[1]</a>, <a href="moose_classes.html#MarkovChannel.getInitialState">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.getInitialState">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getInitialState">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getInitialState">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IzhikevichNrn.getInitU">getInitU() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getInitU">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getInitU">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.getInitVm">getInitVm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getInitVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getInitVm">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.getInitVm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getInitVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getInitVm">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.getInject">getInject() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getInject">[1]</a>, <a href="moose_classes.html#CompartmentBase.getInject">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.getInject">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getInject">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getInject">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.getInject">(RC method)</a>, <a href="moose_builtins.html#RC.getInject">[1]</a>, <a href="moose_classes.html#RC.getInject">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#getInnerArea">getInnerArea()</a>, <a href="moose_builtins.html#getInnerArea">[1]</a>, <a href="moose_classes.html#getInnerArea">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.getInputOffset">getInputOffset() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.getInputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.getInputOffset">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.getInstant">getInstant() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getInstant">[1]</a>, <a href="moose_classes.html#HHChannel.getInstant">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.getInstant">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getInstant">[1]</a>, <a href="moose_classes.html#HHChannel2D.getInstant">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getInstant">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getInstant">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getInstant">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PIDController.getIntegral">getIntegral() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getIntegral">[1]</a>, <a href="moose_classes.html#PIDController.getIntegral">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.getInternalDt">getInternalDt() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getInternalDt">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getInternalDt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.getInvdx">getInvdx() (MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getInvdx">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getInvdx">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VectorTable.getInvdx">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getInvdx">[1]</a>, <a href="moose_classes.html#VectorTable.getInvdx">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovSolverBase.getInvdy">getInvdy() (MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getInvdy">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getInvdy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.getIsInitialized">getIsInitialized() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getIsInitialized">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getIsInitialized">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SteadyState.getIsInitialized">(SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getIsInitialized">[1]</a>, <a href="moose_classes.html#SteadyState.getIsInitialized">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.getIsRunning">getIsRunning() (Clock method)</a>, <a href="moose_builtins.html#Clock.getIsRunning">[1]</a>, <a href="moose_classes.html#Clock.getIsRunning">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getIsToroid">getIsToroid() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getIsToroid">[1]</a>, <a href="moose_classes.html#CubeMesh.getIsToroid">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.getK1">getK1() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getK1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.getK2">getK2() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getK2">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getK2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.getK3">getK3() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getK3">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getK3">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.getKb">getKb() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getKb">[1]</a>, <a href="moose_classes.html#ReacBase.getKb">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.getKcat">getKcat() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.getKcat">[1]</a>, <a href="moose_classes.html#EnzBase.getKcat">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.getKf">getKf() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getKf">[1]</a>, <a href="moose_classes.html#ReacBase.getKf">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.getKm">getKm() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.getKm">[1]</a>, <a href="moose_classes.html#EnzBase.getKm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.getKMg_A">getKMg_A() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getKMg_A">[1]</a>, <a href="moose_classes.html#MgBlock.getKMg_A">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.getKMg_B">getKMg_B() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getKMg_B">[1]</a>, <a href="moose_classes.html#MgBlock.getKMg_B">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.getKsolve">getKsolve() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getKsolve">[1]</a>, <a href="moose_classes.html#Stoich.getKsolve">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.getLabels">getLabels() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getLabels">[1]</a>, <a href="moose_classes.html#MarkovChannel.getLabels">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getLeak">getLeak()</a>, <a href="moose_builtins.html#getLeak">[1]</a>, <a href="moose_classes.html#getLeak">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getLength">getLength()</a>, <a href="moose_builtins.html#getLength">[1]</a>, <a href="moose_classes.html#getLength">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.getLength">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getLength">[1]</a>, <a href="moose_classes.html#CompartmentBase.getLength">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.getLevel">getLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getLevel">[1]</a>, <a href="moose_classes.html#PulseGen.getLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.getLigandConc">getLigandConc() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getLigandConc">[1]</a>, <a href="moose_classes.html#MarkovChannel.getLigandConc">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovRateTable.getLigandConc">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.getLigandConc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.getLigandConc">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#VectorTable.getLookupindex">getLookupindex() (VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getLookupindex">[1]</a>, <a href="moose_classes.html#VectorTable.getLookupindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.getLookupvalue">getLookupvalue() (VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getLookupvalue">[1]</a>, <a href="moose_classes.html#VectorTable.getLookupvalue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.getLoopTime">getLoopTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getLoopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.getLoopTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MathFunc.getMathML">getMathML() (MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.getMathML">[1]</a>, <a href="moose_classes.html#MathFunc.getMathML">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.getMatrixEntry">getMatrixEntry() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getMatrixEntry">[1]</a>, <a href="moose_classes.html#Stoich.getMatrixEntry">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.getMax">getMax() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getMax">[1]</a>, <a href="moose_classes.html#HHGate.getMax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getMaxIter">getMaxIter() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getMaxIter">[1]</a>, <a href="moose_classes.html#SteadyState.getMaxIter">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getMe">getMe() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMe">[1]</a>, <a href="moose_classes.html#Neutral.getMe">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats.getMean">getMean() (Stats method)</a>, <a href="moose_builtins.html#Stats.getMean">[1]</a>, <a href="moose_classes.html#Stats.getMean">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getMeshToSpace">getMeshToSpace() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getMeshToSpace">[1]</a>, <a href="moose_classes.html#CubeMesh.getMeshToSpace">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.getMeshType">getMeshType() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getMeshType">[1]</a>, <a href="moose_classes.html#MeshEntry.getMeshType">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.getMethod">getMethod() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getMethod">[1]</a>, <a href="moose_classes.html#Ksolve.getMethod">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovGslSolver.getMethod">(MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getMethod">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getMethod">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.getMethod">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.getMethod">[1]</a>, <a href="moose_classes.html#TimeTable.getMethod">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.getMin">getMin() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getMin">[1]</a>, <a href="moose_classes.html#HHGate.getMin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.getMInfinity">getMInfinity() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getMInfinity">[1]</a>, <a href="moose_classes.html#HHGate.getMInfinity">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.getMode">getMode() (Func method)</a>, <a href="moose_builtins.html#Func.getMode">[1]</a>, <a href="moose_classes.html#Func.getMode">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VClamp.getMode">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getMode">[1]</a>, <a href="moose_classes.html#VClamp.getMode">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Species.getMolWt">getMolWt() (Species method)</a>, <a href="moose_builtins.html#Species.getMolWt">[1]</a>, <a href="moose_classes.html#Species.getMolWt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.getMotorConst">getMotorConst() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getMotorConst">[1]</a>, <a href="moose_classes.html#PoolBase.getMotorConst">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getMsgDestFunctions">getMsgDestFunctions() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMsgDestFunctions">[1]</a>, <a href="moose_classes.html#Neutral.getMsgDestFunctions">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getMsgDests">getMsgDests() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMsgDests">[1]</a>, <a href="moose_classes.html#Neutral.getMsgDests">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getMsgIn">getMsgIn() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMsgIn">[1]</a>, <a href="moose_classes.html#Neutral.getMsgIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getMsgOut">getMsgOut() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getMsgOut">[1]</a>, <a href="moose_classes.html#Neutral.getMsgOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PostMaster.getMyNode">getMyNode() (PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.getMyNode">[1]</a>, <a href="moose_classes.html#PostMaster.getMyNode">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.getN">getN() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getN">[1]</a>, <a href="moose_classes.html#PoolBase.getN">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getName">getName() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getName">[1]</a>, <a href="moose_classes.html#Neutral.getName">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.getNeighbors">getNeighbors() (MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.getNeighbors">[1]</a>, <a href="moose_classes.html#MeshEntry.getNeighbors">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Neutral.getNeighbors">(Neutral method)</a>, <a href="moose_builtins.html#Neutral.getNeighbors">[1]</a>, <a href="moose_classes.html#Neutral.getNeighbors">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PoolBase.getNInit">getNInit() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getNInit">[1]</a>, <a href="moose_classes.html#PoolBase.getNInit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getNIter">getNIter() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getNIter">[1]</a>, <a href="moose_classes.html#SteadyState.getNIter">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getNNegEigenvalues">getNNegEigenvalues() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getNNegEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.getNNegEigenvalues">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.getNormalizeWeights">getNormalizeWeights() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.getNormalizeWeights">[1]</a>, <a href="moose_classes.html#SynChan.getNormalizeWeights">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.getNotes">getNotes() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getNotes">[1]</a>, <a href="moose_classes.html#Annotator.getNotes">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getNPosEigenvalues">getNPosEigenvalues() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getNPosEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.getNPosEigenvalues">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.getNsteps">getNsteps() (Clock method)</a>, <a href="moose_builtins.html#Clock.getNsteps">[1]</a>, <a href="moose_classes.html#Clock.getNsteps">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats.getNum">getNum() (Stats method)</a>, <a href="moose_builtins.html#Stats.getNum">[1]</a>, <a href="moose_classes.html#Stats.getNum">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.getNumAllPools">getNumAllPools() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getNumAllPools">[1]</a>, <a href="moose_classes.html#Stoich.getNumAllPools">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.getNumAllVoxels">getNumAllVoxels() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getNumAllVoxels">[1]</a>, <a href="moose_classes.html#Dsolve.getNumAllVoxels">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.getNumAllVoxels">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getNumAllVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.getNumAllVoxels">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.getNumAllVoxels">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getNumAllVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.getNumAllVoxels">[2]</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#SparseMsg.getNumColumns">getNumColumns() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getNumColumns">[1]</a>, <a href="moose_classes.html#SparseMsg.getNumColumns">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getNumData">getNumData() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getNumData">[1]</a>, <a href="moose_classes.html#Neutral.getNumData">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.getNumDiffCompts">getNumDiffCompts() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getNumDiffCompts">[1]</a>, <a href="moose_classes.html#CylMesh.getNumDiffCompts">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#NeuroMesh.getNumDiffCompts">(NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getNumDiffCompts">[1]</a>, <a href="moose_classes.html#NeuroMesh.getNumDiffCompts">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChemCompt.getNumDimensions">getNumDimensions() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getNumDimensions">[1]</a>, <a href="moose_classes.html#ChemCompt.getNumDimensions">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.getNumEntries">getNumEntries() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getNumEntries">[1]</a>, <a href="moose_classes.html#SparseMsg.getNumEntries">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getNumField">getNumField() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getNumField">[1]</a>, <a href="moose_classes.html#Neutral.getNumField">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.getNumGateX">getNumGateX() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getNumGateX">[1]</a>, <a href="moose_classes.html#HHChannel.getNumGateX">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.getNumGateX">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getNumGateX">[1]</a>, <a href="moose_classes.html#HHChannel2D.getNumGateX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getNumGateX">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getNumGateX">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getNumGateX">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel.getNumGateY">getNumGateY() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getNumGateY">[1]</a>, <a href="moose_classes.html#HHChannel.getNumGateY">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.getNumGateY">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getNumGateY">[1]</a>, <a href="moose_classes.html#HHChannel2D.getNumGateY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getNumGateY">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getNumGateY">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getNumGateY">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel.getNumGateZ">getNumGateZ() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getNumGateZ">[1]</a>, <a href="moose_classes.html#HHChannel.getNumGateZ">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.getNumGateZ">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getNumGateZ">[1]</a>, <a href="moose_classes.html#HHChannel2D.getNumGateZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getNumGateZ">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getNumGateZ">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getNumGateZ">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ReacBase.getNumKb">getNumKb() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getNumKb">[1]</a>, <a href="moose_classes.html#ReacBase.getNumKb">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.getNumKf">getNumKf() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getNumKf">[1]</a>, <a href="moose_classes.html#ReacBase.getNumKf">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.getNumKm">getNumKm() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.getNumKm">[1]</a>, <a href="moose_classes.html#EnzBase.getNumKm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve.getNumLocalVoxels">getNumLocalVoxels() (Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getNumLocalVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.getNumLocalVoxels">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Ksolve.getNumLocalVoxels">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getNumLocalVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.getNumLocalVoxels">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChemCompt.getNumMesh">getNumMesh() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getNumMesh">[1]</a>, <a href="moose_classes.html#ChemCompt.getNumMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PostMaster.getNumNodes">getNumNodes() (PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.getNumNodes">[1]</a>, <a href="moose_classes.html#PostMaster.getNumNodes">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.getNumOpenStates">getNumOpenStates() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getNumOpenStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.getNumOpenStates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.getNumPools">getNumPools() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getNumPools">[1]</a>, <a href="moose_classes.html#Dsolve.getNumPools">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.getNumPools">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getNumPools">[1]</a>, <a href="moose_classes.html#Gsolve.getNumPools">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.getNumPools">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getNumPools">[1]</a>, <a href="moose_classes.html#Ksolve.getNumPools">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ReacBase.getNumProducts">getNumProducts() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getNumProducts">[1]</a>, <a href="moose_classes.html#ReacBase.getNumProducts">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.getNumRates">getNumRates() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getNumRates">[1]</a>, <a href="moose_classes.html#Stoich.getNumRates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.getNumRows">getNumRows() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getNumRows">[1]</a>, <a href="moose_classes.html#SparseMsg.getNumRows">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh.getNumSegments">getNumSegments() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getNumSegments">[1]</a>, <a href="moose_classes.html#NeuroMesh.getNumSegments">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.getNumStates">getNumStates() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getNumStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.getNumStates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.getNumSubstrates">getNumSubstrates() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.getNumSubstrates">[1]</a>, <a href="moose_classes.html#EnzBase.getNumSubstrates">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ReacBase.getNumSubstrates">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.getNumSubstrates">[1]</a>, <a href="moose_classes.html#ReacBase.getNumSubstrates">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SynHandler.getNumSynapse">getNumSynapse() (SynHandler method)</a>, <a href="moose_builtins.html#SynHandler.getNumSynapse">[1]</a>, <a href="moose_classes.html#SynHandler.getNumSynapse">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynHandler.getNumSynapses">getNumSynapses() (SynHandler method)</a>, <a href="moose_builtins.html#SynHandler.getNumSynapses">[1]</a>, <a href="moose_classes.html#SynHandler.getNumSynapses">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.getNumTicks">getNumTicks() (Clock method)</a>, <a href="moose_builtins.html#Clock.getNumTicks">[1]</a>, <a href="moose_classes.html#Clock.getNumTicks">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getNumVarPools">getNumVarPools() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getNumVarPools">[1]</a>, <a href="moose_classes.html#SteadyState.getNumVarPools">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Stoich.getNumVarPools">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.getNumVarPools">[1]</a>, <a href="moose_classes.html#Stoich.getNumVarPools">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Dsolve.getNumVoxels">getNumVoxels() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getNumVoxels">[1]</a>, <a href="moose_classes.html#Dsolve.getNumVoxels">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.getNVec">getNVec() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getNVec">[1]</a>, <a href="moose_classes.html#Dsolve.getNVec">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.getNVec">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getNVec">[1]</a>, <a href="moose_classes.html#Gsolve.getNVec">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.getNVec">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getNVec">[1]</a>, <a href="moose_classes.html#Ksolve.getNVec">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.getNx">getNx() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getNx">[1]</a>, <a href="moose_classes.html#CubeMesh.getNx">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getNy">getNy() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getNy">[1]</a>, <a href="moose_classes.html#CubeMesh.getNy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getNz">getNz() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getNz">[1]</a>, <a href="moose_classes.html#CubeMesh.getNz">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChemCompt.getOneVoxelVolume">getOneVoxelVolume() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getOneVoxelVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.getOneVoxelVolume">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getOuterArea">getOuterArea()</a>, <a href="moose_builtins.html#getOuterArea">[1]</a>, <a href="moose_classes.html#getOuterArea">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.getOutputOffset">getOutputOffset() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.getOutputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.getOutputOffset">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.getOutputValue">getOutputValue() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.getOutputValue">[1]</a>, <a href="moose_classes.html#Adaptor.getOutputValue">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Arith.getOutputValue">(Arith method)</a>, <a href="moose_builtins.html#Arith.getOutputValue">[1]</a>, <a href="moose_classes.html#Arith.getOutputValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.getOutputValue">(DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.getOutputValue">[1]</a>, <a href="moose_classes.html#DiffAmp.getOutputValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.getOutputValue">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.getOutputValue">[1]</a>, <a href="moose_classes.html#PIDController.getOutputValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getOutputValue">(PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getOutputValue">[1]</a>, <a href="moose_classes.html#PulseGen.getOutputValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.getOutputValue">(TableBase method)</a>, <a href="moose_builtins.html#TableBase.getOutputValue">[1]</a>, <a href="moose_classes.html#TableBase.getOutputValue">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Neutral.getParent">getParent() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getParent">[1]</a>, <a href="moose_classes.html#Neutral.getParent">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh.getParentVoxel">getParentVoxel() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getParentVoxel">[1]</a>, <a href="moose_classes.html#NeuroMesh.getParentVoxel">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SpineMesh.getParentVoxel">(SpineMesh method)</a>, <a href="moose_builtins.html#SpineMesh.getParentVoxel">[1]</a>, <a href="moose_classes.html#SpineMesh.getParentVoxel">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Dsolve.getPath">getPath() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getPath">[1]</a>, <a href="moose_classes.html#Dsolve.getPath">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Neutral.getPath">(Neutral method)</a>, <a href="moose_builtins.html#Neutral.getPath">[1]</a>, <a href="moose_classes.html#Neutral.getPath">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.getPath">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.getPath">[1]</a>, <a href="moose_classes.html#Stoich.getPath">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Stoich.getPoolIdMap">getPoolIdMap() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getPoolIdMap">[1]</a>, <a href="moose_classes.html#Stoich.getPoolIdMap">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getPreserveNumEntries">getPreserveNumEntries() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getPreserveNumEntries">[1]</a>, <a href="moose_classes.html#CubeMesh.getPreserveNumEntries">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.getProbability">getProbability() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getProbability">[1]</a>, <a href="moose_classes.html#SparseMsg.getProbability">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.getQ">getQ() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.getQ">[1]</a>, <a href="moose_classes.html#MarkovRateTable.getQ">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.getQ">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getQ">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getQ">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#RC.getR">getR() (RC method)</a>, <a href="moose_builtins.html#RC.getR">[1]</a>, <a href="moose_classes.html#RC.getR">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.getR0">getR0() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getR0">[1]</a>, <a href="moose_classes.html#CylMesh.getR0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.getR1">getR1() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getR1">[1]</a>, <a href="moose_classes.html#CylMesh.getR1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.getRa">getRa() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getRa">[1]</a>, <a href="moose_classes.html#CompartmentBase.getRa">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getRank">getRank() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getRank">[1]</a>, <a href="moose_classes.html#SteadyState.getRank">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.getRatio">getRatio() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.getRatio">[1]</a>, <a href="moose_classes.html#CplxEnzBase.getRatio">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.getRefractoryPeriod">getRefractoryPeriod() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.getRefractoryPeriod">[1]</a>, <a href="moose_classes.html#IntFire.getRefractoryPeriod">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.getRefractT">getRefractT() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getRefractT">[1]</a>, <a href="moose_classes.html#SpikeGen.getRefractT">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.getRelativeAccuracy">getRelativeAccuracy() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.getRelativeAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.getRelativeAccuracy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#FuncBase.getResult">getResult() (FuncBase method)</a>, <a href="moose_builtins.html#FuncBase.getResult">[1]</a>, <a href="moose_classes.html#FuncBase.getResult">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MathFunc.getResult">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.getResult">[1]</a>, <a href="moose_classes.html#MathFunc.getResult">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.getRm">getRm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getRm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getRm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.getRmByTau">getRmByTau() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getRmByTau">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getRmByTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.getRowStart">getRowStart() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.getRowStart">[1]</a>, <a href="moose_classes.html#Stoich.getRowStart">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.getRunTime">getRunTime() (Clock method)</a>, <a href="moose_builtins.html#Clock.getRunTime">[1]</a>, <a href="moose_classes.html#Clock.getRunTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.getSaturation">getSaturation() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.getSaturation">[1]</a>, <a href="moose_classes.html#DiffAmp.getSaturation">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#PIDController.getSaturation">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.getSaturation">[1]</a>, <a href="moose_classes.html#PIDController.getSaturation">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Adaptor.getScale">getScale() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.getScale">[1]</a>, <a href="moose_classes.html#Adaptor.getScale">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Nernst.getScale">(Nernst method)</a>, <a href="moose_builtins.html#Nernst.getScale">[1]</a>, <a href="moose_classes.html#Nernst.getScale">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Stats.getSdev">getSdev() (Stats method)</a>, <a href="moose_builtins.html#Stats.getSdev">[1]</a>, <a href="moose_classes.html#Stats.getSdev">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getSecondDelay">getSecondDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getSecondDelay">[1]</a>, <a href="moose_classes.html#PulseGen.getSecondDelay">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getSecondLevel">getSecondLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getSecondLevel">[1]</a>, <a href="moose_classes.html#PulseGen.getSecondLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getSecondWidth">getSecondWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getSecondWidth">[1]</a>, <a href="moose_classes.html#PulseGen.getSecondWidth">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.getSeed">getSeed() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getSeed">[1]</a>, <a href="moose_classes.html#HSolve.getSeed">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SparseMsg.getSeed">(SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.getSeed">[1]</a>, <a href="moose_classes.html#SparseMsg.getSeed">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PIDController.getSensed">getSensed() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getSensed">[1]</a>, <a href="moose_classes.html#PIDController.getSensed">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VClamp.getSensed">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getSensed">[1]</a>, <a href="moose_classes.html#VClamp.getSensed">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.getSeparateSpines">getSeparateSpines() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getSeparateSpines">[1]</a>, <a href="moose_classes.html#NeuroMesh.getSeparateSpines">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getShapeMode">getShapeMode()</a>, <a href="moose_builtins.html#getShapeMode">[1]</a>, <a href="moose_classes.html#getShapeMode">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.getSize">getSize() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.getSize">[1]</a>, <a href="moose_classes.html#MarkovRateTable.getSize">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#TableBase.getSize">(TableBase method)</a>, <a href="moose_builtins.html#TableBase.getSize">[1]</a>, <a href="moose_classes.html#TableBase.getSize">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SteadyState.getSolutionStatus">getSolutionStatus() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getSolutionStatus">[1]</a>, <a href="moose_classes.html#SteadyState.getSolutionStatus">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.getSourceFields">getSourceFields() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getSourceFields">[1]</a>, <a href="moose_classes.html#Neutral.getSourceFields">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getSpaceToMesh">getSpaceToMesh() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getSpaceToMesh">[1]</a>, <a href="moose_classes.html#CubeMesh.getSpaceToMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.getSpeciesId">getSpeciesId() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getSpeciesId">[1]</a>, <a href="moose_classes.html#PoolBase.getSpeciesId">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Finfo.getSrc">getSrc() (Finfo method)</a>, <a href="moose_builtins.html#Finfo.getSrc">[1]</a>, <a href="moose_classes.html#Finfo.getSrc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.getSrcFieldsOnE1">getSrcFieldsOnE1() (Msg method)</a>, <a href="moose_builtins.html#Msg.getSrcFieldsOnE1">[1]</a>, <a href="moose_classes.html#Msg.getSrcFieldsOnE1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.getSrcFieldsOnE2">getSrcFieldsOnE2() (Msg method)</a>, <a href="moose_builtins.html#Msg.getSrcFieldsOnE2">[1]</a>, <a href="moose_classes.html#Msg.getSrcFieldsOnE2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.getStartTime">getStartTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getStartTime">[1]</a>, <a href="moose_classes.html#StimulusTable.getStartTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.getState">getState() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getState">[1]</a>, <a href="moose_classes.html#MarkovChannel.getState">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.getState">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getState">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getState">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.getState">(RC method)</a>, <a href="moose_builtins.html#RC.getState">[1]</a>, <a href="moose_classes.html#RC.getState">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.getState">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.getState">[1]</a>, <a href="moose_classes.html#TimeTable.getState">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SteadyState.getStateType">getStateType() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getStateType">[1]</a>, <a href="moose_classes.html#SteadyState.getStateType">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getStatus">getStatus() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getStatus">[1]</a>, <a href="moose_classes.html#SteadyState.getStatus">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChemCompt.getStencilIndex">getStencilIndex() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getStencilIndex">[1]</a>, <a href="moose_classes.html#ChemCompt.getStencilIndex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChemCompt.getStencilRate">getStencilRate() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getStencilRate">[1]</a>, <a href="moose_classes.html#ChemCompt.getStencilRate">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.getStepPosition">getStepPosition() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getStepPosition">[1]</a>, <a href="moose_classes.html#StimulusTable.getStepPosition">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.getStepSize">getStepSize() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getStepSize">[1]</a>, <a href="moose_classes.html#StimulusTable.getStepSize">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.getStoich">getStoich() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.getStoich">[1]</a>, <a href="moose_classes.html#Dsolve.getStoich">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.getStoich">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getStoich">[1]</a>, <a href="moose_classes.html#Gsolve.getStoich">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.getStoich">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.getStoich">[1]</a>, <a href="moose_classes.html#Ksolve.getStoich">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getStoich">(SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getStoich">[1]</a>, <a href="moose_classes.html#SteadyState.getStoich">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#StimulusTable.getStopTime">getStopTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.getStopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.getStopTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiagonalMsg.getStride">getStride() (DiagonalMsg method)</a>, <a href="moose_builtins.html#DiagonalMsg.getStride">[1]</a>, <a href="moose_classes.html#DiagonalMsg.getStride">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh.getSubTree">getSubTree() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.getSubTree">[1]</a>, <a href="moose_classes.html#NeuroMesh.getSubTree">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats.getSum">getSum() (Stats method)</a>, <a href="moose_builtins.html#Stats.getSum">[1]</a>, <a href="moose_classes.html#Stats.getSum">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.getSurface">getSurface() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getSurface">[1]</a>, <a href="moose_classes.html#CubeMesh.getSurface">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.getTable">getTable() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getTable">[1]</a>, <a href="moose_classes.html#Interpol2D.getTable">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VectorTable.getTable">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getTable">[1]</a>, <a href="moose_classes.html#VectorTable.getTable">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.getTableA">getTableA() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getTableA">[1]</a>, <a href="moose_classes.html#HHGate.getTableA">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate2D.getTableA">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getTableA">[1]</a>, <a href="moose_classes.html#HHGate2D.getTableA">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.getTableB">getTableB() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getTableB">[1]</a>, <a href="moose_classes.html#HHGate.getTableB">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate2D.getTableB">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getTableB">[1]</a>, <a href="moose_classes.html#HHGate2D.getTableB">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.getTableVector2D">getTableVector2D() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getTableVector2D">[1]</a>, <a href="moose_classes.html#Interpol2D.getTableVector2D">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.getTarget">getTarget() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getTarget">[1]</a>, <a href="moose_classes.html#HSolve.getTarget">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.getTau">getTau() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getTau">[1]</a>, <a href="moose_classes.html#CaConc.getTau">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate.getTau">(HHGate method)</a>, <a href="moose_builtins.html#HHGate.getTau">[1]</a>, <a href="moose_classes.html#HHGate.getTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.getTau">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.getTau">[1]</a>, <a href="moose_classes.html#IntFire.getTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.getTau">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.getTau">[1]</a>, <a href="moose_classes.html#VClamp.getTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCaConc.getTau">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getTau">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getTau">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SynChan.getTau1">getTau1() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.getTau1">[1]</a>, <a href="moose_classes.html#SynChan.getTau1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.getTau2">getTau2() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.getTau2">[1]</a>, <a href="moose_classes.html#SynChan.getTau2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.getTauD">getTauD() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getTauD">[1]</a>, <a href="moose_classes.html#PIDController.getTauD">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.getTauI">getTauI() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.getTauI">[1]</a>, <a href="moose_classes.html#PIDController.getTauI">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.getTd">getTd() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.getTd">[1]</a>, <a href="moose_classes.html#VClamp.getTd">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.getTemperature">getTemperature() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.getTemperature">[1]</a>, <a href="moose_classes.html#Nernst.getTemperature">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.getTextColor">getTextColor() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getTextColor">[1]</a>, <a href="moose_classes.html#Annotator.getTextColor">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.getThick">getThick() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.getThick">[1]</a>, <a href="moose_classes.html#CaConc.getThick">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.getThick">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.getThick">[1]</a>, <a href="moose_classes.html#ZombieCaConc.getThick">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#getThickness">getThickness()</a>, <a href="moose_builtins.html#getThickness">[1]</a>, <a href="moose_classes.html#getThickness">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#PsdMesh.getThickness">(PsdMesh method)</a>, <a href="moose_builtins.html#PsdMesh.getThickness">[1]</a>, <a href="moose_classes.html#PsdMesh.getThickness">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Mstring.getThis">getThis() (Mstring method)</a>, <a href="moose_builtins.html#Mstring.getThis">[1]</a>, <a href="moose_classes.html#Mstring.getThis">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Neutral.getThis">(Neutral method)</a>, <a href="moose_builtins.html#Neutral.getThis">[1]</a>, <a href="moose_classes.html#Neutral.getThis">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IntFire.getThresh">getThresh() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.getThresh">[1]</a>, <a href="moose_classes.html#IntFire.getThresh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.getThreshold">getThreshold() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.getThreshold">[1]</a>, <a href="moose_classes.html#SpikeGen.getThreshold">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Table.getThreshold">(Table method)</a>, <a href="moose_builtins.html#Table.getThreshold">[1]</a>, <a href="moose_classes.html#Table.getThreshold">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#VClamp.getTi">getTi() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.getTi">[1]</a>, <a href="moose_classes.html#VClamp.getTi">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.getTickDt">getTickDt() (Clock method)</a>, <a href="moose_builtins.html#Clock.getTickDt">[1]</a>, <a href="moose_classes.html#Clock.getTickDt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.getTickStep">getTickStep() (Clock method)</a>, <a href="moose_builtins.html#Clock.getTickStep">[1]</a>, <a href="moose_classes.html#Clock.getTickStep">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.getTotal">getTotal() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.getTotal">[1]</a>, <a href="moose_classes.html#SteadyState.getTotal">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.getTotLength">getTotLength() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getTotLength">[1]</a>, <a href="moose_classes.html#CylMesh.getTotLength">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getTrigMode">getTrigMode() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getTrigMode">[1]</a>, <a href="moose_classes.html#PulseGen.getTrigMode">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Finfo.getType">getType() (Finfo method)</a>, <a href="moose_builtins.html#Finfo.getType">[1]</a>, <a href="moose_classes.html#Finfo.getType">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.getU">getU() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getU">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getU">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.getU0">getU0() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getU0">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getU0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.getUseConcentration">getUseConcentration() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getUseConcentration">[1]</a>, <a href="moose_classes.html#HHChannel.getUseConcentration">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieHHChannel.getUseConcentration">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getUseConcentration">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getUseConcentration">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.getUseInterpolation">getUseInterpolation() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.getUseInterpolation">[1]</a>, <a href="moose_classes.html#HHGate.getUseInterpolation">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve.getUseRandInit">getUseRandInit() (Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.getUseRandInit">[1]</a>, <a href="moose_classes.html#Gsolve.getUseRandInit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.getV0">getV0() (RC method)</a>, <a href="moose_builtins.html#RC.getV0">[1]</a>, <a href="moose_classes.html#RC.getV0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getValence">getValence()</a>, <a href="moose_builtins.html#getValence">[1]</a>, <a href="moose_classes.html#getValence">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Nernst.getValence">(Nernst method)</a>, <a href="moose_builtins.html#Nernst.getValence">[1]</a>, <a href="moose_classes.html#Nernst.getValence">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Double.getValue">getValue() (Double method)</a>, <a href="moose_builtins.html#Double.getValue">[1]</a>, <a href="moose_classes.html#Double.getValue">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Func.getValue">(Func method)</a>, <a href="moose_builtins.html#Func.getValue">[1]</a>, <a href="moose_classes.html#Func.getValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Long.getValue">(Long method)</a>, <a href="moose_builtins.html#Long.getValue">[1]</a>, <a href="moose_classes.html#Long.getValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Mstring.getValue">(Mstring method)</a>, <a href="moose_builtins.html#Mstring.getValue">[1]</a>, <a href="moose_classes.html#Mstring.getValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Unsigned.getValue">(Unsigned method)</a>, <a href="moose_builtins.html#Unsigned.getValue">[1]</a>, <a href="moose_classes.html#Unsigned.getValue">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Neutral.getValueFields">getValueFields() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.getValueFields">[1]</a>, <a href="moose_classes.html#Neutral.getValueFields">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.getVar">getVar() (Func method)</a>, <a href="moose_builtins.html#Func.getVar">[1]</a>, <a href="moose_classes.html#Func.getVar">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.getVars">getVars() (Func method)</a>, <a href="moose_builtins.html#Func.getVars">[1]</a>, <a href="moose_classes.html#Func.getVars">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.getVDiv">getVDiv() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getVDiv">[1]</a>, <a href="moose_classes.html#HSolve.getVDiv">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.getVector">getVector() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.getVector">[1]</a>, <a href="moose_classes.html#TableBase.getVector">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.getVm">getVm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.getVm">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IntFire.getVm">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.getVm">[1]</a>, <a href="moose_classes.html#IntFire.getVm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.getVm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getVm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.getVm">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.getVm">[1]</a>, <a href="moose_classes.html#MarkovChannel.getVm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.getVm">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.getVm">[1]</a>, <a href="moose_classes.html#MarkovRateTable.getVm">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HSolve.getVMax">getVMax() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getVMax">[1]</a>, <a href="moose_classes.html#HSolve.getVMax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.getVmax">getVmax() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.getVmax">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.getVmax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.getVMin">getVMin() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.getVMin">[1]</a>, <a href="moose_classes.html#HSolve.getVMin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#getVolume">getVolume()</a>, <a href="moose_builtins.html#getVolume">[1]</a>, <a href="moose_classes.html#getVolume">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ChemCompt.getVolume">(ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.getVolume">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.getVolume">(MeshEntry method)</a>, <a href="tmp.html#MeshEntry.getVolume">[1]</a>, <a href="moose_builtins.html#MeshEntry.getVolume">[2]</a>, <a href="moose_builtins.html#MeshEntry.getVolume">[3]</a>, <a href="moose_classes.html#MeshEntry.getVolume">[4]</a>, <a href="moose_classes.html#MeshEntry.getVolume">[5]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.getVolume">(PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.getVolume">[1]</a>, <a href="moose_classes.html#PoolBase.getVolume">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChemCompt.getVoxelVolume">getVoxelVolume() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.getVoxelVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.getVoxelVolume">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Synapse.getWeight">getWeight() (Synapse method)</a>, <a href="moose_builtins.html#Synapse.getWeight">[1]</a>, <a href="moose_classes.html#Synapse.getWeight">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.getWidth">getWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.getWidth">[1]</a>, <a href="moose_classes.html#PulseGen.getWidth">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.getX">getX() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getX">[1]</a>, <a href="moose_classes.html#Annotator.getX">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.getX">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getX">[1]</a>, <a href="moose_classes.html#CompartmentBase.getX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.getX">(Func method)</a>, <a href="moose_builtins.html#Func.getX">[1]</a>, <a href="moose_classes.html#Func.getX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.getX">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getX">[1]</a>, <a href="moose_classes.html#HHChannel.getX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.getX">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getX">[1]</a>, <a href="moose_classes.html#HHChannel2D.getX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getX">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getX">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getX">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.getX0">getX0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getX0">[1]</a>, <a href="moose_classes.html#CompartmentBase.getX0">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CubeMesh.getX0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getX0">[1]</a>, <a href="moose_classes.html#CubeMesh.getX0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.getX0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getX0">[1]</a>, <a href="moose_classes.html#CylMesh.getX0">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.getX1">getX1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getX1">[1]</a>, <a href="moose_classes.html#CubeMesh.getX1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.getX1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getX1">[1]</a>, <a href="moose_classes.html#CylMesh.getX1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.getXdivs">getXdivs() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getXdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.getXdivs">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.getXdivs">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getXdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getXdivs">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.getXdivs">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getXdivs">[1]</a>, <a href="moose_classes.html#VectorTable.getXdivs">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.getXdivsA">getXdivsA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.getXdivsA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.getXdivsB">getXdivsB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.getXdivsB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.getXindex">getXindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getXindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.getXindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.getXmax">getXmax() (Interpol method)</a>, <a href="moose_builtins.html#Interpol.getXmax">[1]</a>, <a href="moose_classes.html#Interpol.getXmax">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.getXmax">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getXmax">[1]</a>, <a href="moose_classes.html#Interpol2D.getXmax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.getXmax">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getXmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getXmax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.getXmax">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getXmax">[1]</a>, <a href="moose_classes.html#VectorTable.getXmax">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.getXmaxA">getXmaxA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.getXmaxA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.getXmaxB">getXmaxB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.getXmaxB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.getXmin">getXmin() (Interpol method)</a>, <a href="moose_builtins.html#Interpol.getXmin">[1]</a>, <a href="moose_classes.html#Interpol.getXmin">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.getXmin">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getXmin">[1]</a>, <a href="moose_classes.html#Interpol2D.getXmin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.getXmin">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getXmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getXmin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.getXmin">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.getXmin">[1]</a>, <a href="moose_classes.html#VectorTable.getXmin">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.getXminA">getXminA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXminA">[1]</a>, <a href="moose_classes.html#HHGate2D.getXminA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.getXminB">getXminB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getXminB">[1]</a>, <a href="moose_classes.html#HHGate2D.getXminB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.getXpower">getXpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getXpower">[1]</a>, <a href="moose_classes.html#HHChannel.getXpower">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.getXpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getXpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.getXpower">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getXpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getXpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getXpower">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Annotator.getY">getY() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getY">[1]</a>, <a href="moose_classes.html#Annotator.getY">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.getY">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getY">[1]</a>, <a href="moose_classes.html#CompartmentBase.getY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.getY">(Func method)</a>, <a href="moose_builtins.html#Func.getY">[1]</a>, <a href="moose_classes.html#Func.getY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.getY">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getY">[1]</a>, <a href="moose_classes.html#HHChannel.getY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.getY">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getY">[1]</a>, <a href="moose_classes.html#HHChannel2D.getY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.getY">(Interpol method)</a>, <a href="moose_builtins.html#Interpol.getY">[1]</a>, <a href="moose_classes.html#Interpol.getY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.getY">(TableBase method)</a>, <a href="moose_builtins.html#TableBase.getY">[1]</a>, <a href="moose_classes.html#TableBase.getY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getY">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getY">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getY">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.getY0">getY0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getY0">[1]</a>, <a href="moose_classes.html#CompartmentBase.getY0">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CubeMesh.getY0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getY0">[1]</a>, <a href="moose_classes.html#CubeMesh.getY0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.getY0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getY0">[1]</a>, <a href="moose_classes.html#CylMesh.getY0">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.getY1">getY1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getY1">[1]</a>, <a href="moose_classes.html#CubeMesh.getY1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.getY1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getY1">[1]</a>, <a href="moose_classes.html#CylMesh.getY1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.getYdivs">getYdivs() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getYdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.getYdivs">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.getYdivs">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getYdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getYdivs">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.getYdivsA">getYdivsA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.getYdivsA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.getYdivsB">getYdivsB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.getYdivsB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.getYindex">getYindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getYindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.getYindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.getYmax">getYmax() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getYmax">[1]</a>, <a href="moose_classes.html#Interpol2D.getYmax">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.getYmax">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getYmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getYmax">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.getYmaxA">getYmaxA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.getYmaxA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.getYmaxB">getYmaxB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.getYmaxB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.getYmin">getYmin() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getYmin">[1]</a>, <a href="moose_classes.html#Interpol2D.getYmin">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.getYmin">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.getYmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.getYmin">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.getYminA">getYminA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYminA">[1]</a>, <a href="moose_classes.html#HHGate2D.getYminA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.getYminB">getYminB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.getYminB">[1]</a>, <a href="moose_classes.html#HHGate2D.getYminB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.getYpower">getYpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getYpower">[1]</a>, <a href="moose_classes.html#HHChannel.getYpower">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.getYpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getYpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.getYpower">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getYpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getYpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getYpower">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Annotator.getZ">getZ() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.getZ">[1]</a>, <a href="moose_classes.html#Annotator.getZ">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.getZ">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getZ">[1]</a>, <a href="moose_classes.html#CompartmentBase.getZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.getZ">(Func method)</a>, <a href="moose_builtins.html#Func.getZ">[1]</a>, <a href="moose_classes.html#Func.getZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.getZ">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getZ">[1]</a>, <a href="moose_classes.html#HHChannel.getZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.getZ">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getZ">[1]</a>, <a href="moose_classes.html#HHChannel2D.getZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.getZ">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.getZ">[1]</a>, <a href="moose_classes.html#Interpol2D.getZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getZ">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getZ">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getZ">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.getZ0">getZ0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.getZ0">[1]</a>, <a href="moose_classes.html#CompartmentBase.getZ0">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CubeMesh.getZ0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getZ0">[1]</a>, <a href="moose_classes.html#CubeMesh.getZ0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.getZ0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getZ0">[1]</a>, <a href="moose_classes.html#CylMesh.getZ0">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.getZ1">getZ1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.getZ1">[1]</a>, <a href="moose_classes.html#CubeMesh.getZ1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.getZ1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.getZ1">[1]</a>, <a href="moose_classes.html#CylMesh.getZ1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel2D.getZindex">getZindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getZindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.getZindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.getZk">getZk() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.getZk">[1]</a>, <a href="moose_classes.html#MgBlock.getZk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.getZpower">getZpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.getZpower">[1]</a>, <a href="moose_classes.html#HHChannel.getZpower">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.getZpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.getZpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.getZpower">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.getZpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.getZpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.getZpower">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChanBase.ghk">ghk (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.ghk">[1]</a>, <a href="moose_classes.html#ChanBase.ghk">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.ghk">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.ghk">[1]</a>, <a href="moose_classes.html#SynChanBase.ghk">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Gk">Gk</a>, <a href="moose_builtins.html#Gk">[1]</a>, <a href="moose_classes.html#Gk">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ChanBase.Gk">(ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.Gk">[1]</a>, <a href="moose_classes.html#ChanBase.Gk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.Gk">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.Gk">[1]</a>, <a href="moose_classes.html#SynChanBase.Gk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.Gk">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Gk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Gk">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Group">Group (built-in class)</a>, <a href="moose_builtins.html#Group">[1]</a>, <a href="moose_classes.html#Group">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Group.group">group (Group attribute)</a>, <a href="moose_builtins.html#Group.group">[1]</a>, <a href="moose_classes.html#Group.group">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve">Gsolve (built-in class)</a>, <a href="moose_builtins.html#Gsolve">[1]</a>, <a href="moose_classes.html#Gsolve">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="H">H</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#CompartmentBase.handleAxial">handleAxial() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.handleAxial">[1]</a>, <a href="moose_classes.html#CompartmentBase.handleAxial">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.handleChannel">handleChannel() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.handleChannel">[1]</a>, <a href="moose_classes.html#CompartmentBase.handleChannel">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.handleChannel">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.handleChannel">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.handleChannel">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovChannel.handleLigandConc">handleLigandConc() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.handleLigandConc">[1]</a>, <a href="moose_classes.html#MarkovChannel.handleLigandConc">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovRateTable.handleLigandConc">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.handleLigandConc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.handleLigandConc">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PoolBase.handleMolWt">handleMolWt() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.handleMolWt">[1]</a>, <a href="moose_classes.html#PoolBase.handleMolWt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Species.handleMolWtRequest">handleMolWtRequest() (Species method)</a>, <a href="moose_builtins.html#Species.handleMolWtRequest">[1]</a>, <a href="moose_classes.html#Species.handleMolWtRequest">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.handleQ">handleQ() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.handleQ">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.handleQ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.handleRaxial">handleRaxial() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.handleRaxial">[1]</a>, <a href="moose_classes.html#CompartmentBase.handleRaxial">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.handleState">handleState() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.handleState">[1]</a>, <a href="moose_classes.html#MarkovChannel.handleState">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#MarkovRateTable.handleVm">handleVm() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.handleVm">[1]</a>, <a href="moose_classes.html#MarkovRateTable.handleVm">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.handleVm">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.handleVm">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.handleVm">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SpikeGen.hasFired">hasFired (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.hasFired">[1]</a>, <a href="moose_classes.html#SpikeGen.hasFired">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel">HHChannel (built-in class)</a>, <a href="moose_builtins.html#HHChannel">[1]</a>, <a href="moose_classes.html#HHChannel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D">HHChannel2D (built-in class)</a>, <a href="moose_builtins.html#HHChannel2D">[1]</a>, <a href="moose_classes.html#HHChannel2D">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate">HHGate (built-in class)</a>, <a href="moose_builtins.html#HHGate">[1]</a>, <a href="moose_classes.html#HHGate">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D">HHGate2D (built-in class)</a>, <a href="moose_builtins.html#HHGate2D">[1]</a>, <a href="moose_classes.html#HHGate2D">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#hillPump">hillPump()</a>, <a href="moose_builtins.html#hillPump">[1]</a>, <a href="moose_classes.html#hillPump">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve">HSolve (built-in class)</a>, <a href="moose_builtins.html#HSolve">[1]</a>, <a href="moose_classes.html#HSolve">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="I">I</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#OneToAllMsg.i1">i1 (OneToAllMsg attribute)</a>, <a href="moose_builtins.html#OneToAllMsg.i1">[1]</a>, <a href="moose_classes.html#OneToAllMsg.i1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SingleMsg.i1">(SingleMsg attribute)</a>, <a href="moose_builtins.html#SingleMsg.i1">[1]</a>, <a href="moose_classes.html#SingleMsg.i1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SingleMsg.i2">i2 (SingleMsg attribute)</a>, <a href="moose_builtins.html#SingleMsg.i2">[1]</a>, <a href="moose_classes.html#SingleMsg.i2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.icon">icon (Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.icon">[1]</a>, <a href="moose_classes.html#Annotator.icon">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.Ik">Ik (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.Ik">[1]</a>, <a href="moose_classes.html#ChanBase.Ik">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MgBlock.Ik">(MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.Ik">[1]</a>, <a href="moose_classes.html#MgBlock.Ik">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.Ik">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.Ik">[1]</a>, <a href="moose_classes.html#SynChanBase.Ik">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.Ik">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Ik">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Ik">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChanBase.IkOut">IkOut (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.IkOut">[1]</a>, <a href="moose_classes.html#ChanBase.IkOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.IkOut">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.IkOut">[1]</a>, <a href="moose_classes.html#SynChanBase.IkOut">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.Im">Im (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Im">[1]</a>, <a href="moose_classes.html#CompartmentBase.Im">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.Im">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.Im">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.Im">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CaConc.increase">increase() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.increase">[1]</a>, <a href="moose_classes.html#CaConc.increase">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.increase">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.increase">[1]</a>, <a href="moose_classes.html#ZombieCaConc.increase">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Pool.increment">increment() (Pool method)</a>, <a href="moose_builtins.html#Pool.increment">[1]</a>, <a href="moose_classes.html#Pool.increment">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#influx">influx()</a>, <a href="moose_builtins.html#influx">[1]</a>, <a href="moose_classes.html#influx">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.init">init (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.init">[1]</a>, <a href="moose_classes.html#CompartmentBase.init">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.init">init() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.init">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.init">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovRateTable.init">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.init">[1]</a>, <a href="moose_classes.html#MarkovRateTable.init">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.init">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.init">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.init">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovChannel.initialState">initialState (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.initialState">[1]</a>, <a href="moose_classes.html#MarkovChannel.initialState">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.initialState">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.initialState">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.initialState">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.initProc">initProc() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.initProc">[1]</a>, <a href="moose_classes.html#CompartmentBase.initProc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.initReinit">initReinit() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.initReinit">[1]</a>, <a href="moose_classes.html#CompartmentBase.initReinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.initU">initU (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.initU">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.initU">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.initVm">initVm (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.initVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.initVm">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.initVm">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.initVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.initVm">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.inject">inject (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.inject">[1]</a>, <a href="moose_classes.html#CompartmentBase.inject">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.inject">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.inject">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.inject">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.inject">(RC attribute)</a>, <a href="moose_builtins.html#RC.inject">[1]</a>, <a href="moose_classes.html#RC.inject">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#RC.injectIn">injectIn() (RC method)</a>, <a href="moose_builtins.html#RC.injectIn">[1]</a>, <a href="moose_classes.html#RC.injectIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.injectMsg">injectMsg() (CompartmentBase method)</a>, <a href="tmp.html#CompartmentBase.injectMsg">[1]</a>, <a href="moose_builtins.html#CompartmentBase.injectMsg">[2]</a>, <a href="moose_builtins.html#CompartmentBase.injectMsg">[3]</a>, <a href="moose_classes.html#CompartmentBase.injectMsg">[4]</a>, <a href="moose_classes.html#CompartmentBase.injectMsg">[5]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.injectMsg">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.injectMsg">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.injectMsg">[2]</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#innerArea">innerArea</a>, <a href="moose_builtins.html#innerArea">[1]</a>, <a href="moose_classes.html#innerArea">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#innerDif">innerDif</a>, <a href="moose_builtins.html#innerDif">[1]</a>, <a href="moose_classes.html#innerDif">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#innerDifSourceOut">innerDifSourceOut</a>, <a href="moose_builtins.html#innerDifSourceOut">[1]</a>, <a href="moose_classes.html#innerDifSourceOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.input">input() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.input">[1]</a>, <a href="moose_classes.html#Adaptor.input">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#FuncBase.input">(FuncBase method)</a>, <a href="moose_builtins.html#FuncBase.input">[1]</a>, <a href="moose_classes.html#FuncBase.input">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#FuncPool.input">(FuncPool method)</a>, <a href="moose_builtins.html#FuncPool.input">[1]</a>, <a href="moose_classes.html#FuncPool.input">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.input">(Interpol method)</a>, <a href="moose_builtins.html#Interpol.input">[1]</a>, <a href="moose_classes.html#Interpol.input">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.input">(PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.input">[1]</a>, <a href="moose_classes.html#PulseGen.input">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Table.input">(Table method)</a>, <a href="moose_builtins.html#Table.input">[1]</a>, <a href="moose_classes.html#Table.input">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieFuncPool.input">(ZombieFuncPool method)</a>, <a href="moose_builtins.html#ZombieFuncPool.input">[1]</a>, <a href="moose_classes.html#ZombieFuncPool.input">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Adaptor.inputOffset">inputOffset (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.inputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.inputOffset">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.instant">instant (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.instant">[1]</a>, <a href="moose_classes.html#HHChannel.instant">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.instant">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.instant">[1]</a>, <a href="moose_classes.html#HHChannel2D.instant">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.instant">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.instant">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.instant">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovRateTable.instratesOut">instratesOut (MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.instratesOut">[1]</a>, <a href="moose_classes.html#MarkovRateTable.instratesOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#integral">integral</a>, <a href="moose_builtins.html#integral">[1]</a>, <a href="moose_classes.html#integral">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.internalDt">internalDt (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.internalDt">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.internalDt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol">Interpol (built-in class)</a>, <a href="moose_builtins.html#Interpol">[1]</a>, <a href="moose_classes.html#Interpol">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D">Interpol2D (built-in class)</a>, <a href="moose_builtins.html#Interpol2D">[1]</a>, <a href="moose_classes.html#Interpol2D">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire">IntFire (built-in class)</a>, <a href="moose_builtins.html#IntFire">[1]</a>, <a href="moose_classes.html#IntFire">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.invdx">invdx (MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.invdx">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.invdx">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VectorTable.invdx">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.invdx">[1]</a>, <a href="moose_classes.html#VectorTable.invdx">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovSolverBase.invdy">invdy (MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.invdy">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.invdy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.isInitialized">isInitialized (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.isInitialized">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.isInitialized">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SteadyState.isInitialized">(SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.isInitialized">[1]</a>, <a href="moose_classes.html#SteadyState.isInitialized">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.isRunning">isRunning (Clock attribute)</a>, <a href="moose_builtins.html#Clock.isRunning">[1]</a>, <a href="moose_classes.html#Clock.isRunning">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.isToroid">isToroid (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.isToroid">[1]</a>, <a href="moose_classes.html#CubeMesh.isToroid">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn">IzhikevichNrn (built-in class)</a>, <a href="moose_builtins.html#IzhikevichNrn">[1]</a>, <a href="moose_classes.html#IzhikevichNrn">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="K">K</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#CplxEnzBase.k1">k1 (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.k1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.k1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.k2">k2 (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.k2">[1]</a>, <a href="moose_classes.html#CplxEnzBase.k2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.k3">k3 (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.k3">[1]</a>, <a href="moose_classes.html#CplxEnzBase.k3">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.Kb">Kb (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.Kb">[1]</a>, <a href="moose_classes.html#ReacBase.Kb">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.kcat">kcat (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.kcat">[1]</a>, <a href="moose_classes.html#EnzBase.kcat">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.Kf">Kf (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.Kf">[1]</a>, <a href="moose_classes.html#ReacBase.Kf">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#EnzBase.Km">Km (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.Km">[1]</a>, <a href="moose_classes.html#EnzBase.Km">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.KMg_A">KMg_A (MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.KMg_A">[1]</a>, <a href="moose_classes.html#MgBlock.KMg_A">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.KMg_B">KMg_B (MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.KMg_B">[1]</a>, <a href="moose_classes.html#MgBlock.KMg_B">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve">Ksolve (built-in class)</a>, <a href="moose_builtins.html#Ksolve">[1]</a>, <a href="moose_classes.html#Ksolve">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.ksolve">ksolve (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.ksolve">[1]</a>, <a href="moose_classes.html#Stoich.ksolve">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="L">L</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#MarkovChannel.labels">labels (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.labels">[1]</a>, <a href="moose_classes.html#MarkovChannel.labels">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#leak">leak</a>, <a href="moose_builtins.html#leak">[1]</a>, <a href="moose_classes.html#leak">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Leakage">Leakage (built-in class)</a>, <a href="moose_builtins.html#Leakage">[1]</a>, <a href="moose_classes.html#Leakage">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#length">length</a>, <a href="moose_builtins.html#length">[1]</a>, <a href="moose_classes.html#length">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.length">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.length">[1]</a>, <a href="moose_classes.html#CompartmentBase.length">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.level">level (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.level">[1]</a>, <a href="moose_classes.html#PulseGen.level">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.levelIn">levelIn() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.levelIn">[1]</a>, <a href="moose_classes.html#PulseGen.levelIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.ligandConc">ligandConc (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.ligandConc">[1]</a>, <a href="moose_classes.html#MarkovChannel.ligandConc">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovRateTable.ligandConc">(MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.ligandConc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.ligandConc">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovSolverBase.ligandConc">ligandConc() (MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.ligandConc">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.ligandConc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.linearTransform">linearTransform() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.linearTransform">[1]</a>, <a href="moose_classes.html#TableBase.linearTransform">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.loadCSV">loadCSV() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.loadCSV">[1]</a>, <a href="moose_classes.html#TableBase.loadCSV">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#TableBase.loadXplot">loadXplot() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.loadXplot">[1]</a>, <a href="moose_classes.html#TableBase.loadXplot">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.loadXplotRange">loadXplotRange() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.loadXplotRange">[1]</a>, <a href="moose_classes.html#TableBase.loadXplotRange">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Long">Long (built-in class)</a>, <a href="moose_builtins.html#Long">[1]</a>, <a href="moose_classes.html#Long">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.lookup">lookup() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.lookup">[1]</a>, <a href="moose_classes.html#Interpol2D.lookup">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.lookupindex">lookupindex (VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.lookupindex">[1]</a>, <a href="moose_classes.html#VectorTable.lookupindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.lookupOut">lookupOut (Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.lookupOut">[1]</a>, <a href="moose_classes.html#Interpol.lookupOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.lookupOut">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.lookupOut">[1]</a>, <a href="moose_classes.html#Interpol2D.lookupOut">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.lookupReturn2D">lookupReturn2D (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.lookupReturn2D">[1]</a>, <a href="moose_classes.html#Interpol2D.lookupReturn2D">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.lookupvalue">lookupvalue (VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.lookupvalue">[1]</a>, <a href="moose_classes.html#VectorTable.lookupvalue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.loopTime">loopTime (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.loopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.loopTime">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="M">M</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#MarkovChannel">MarkovChannel (built-in class)</a>, <a href="moose_builtins.html#MarkovChannel">[1]</a>, <a href="moose_classes.html#MarkovChannel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver">MarkovGslSolver (built-in class)</a>, <a href="moose_builtins.html#MarkovGslSolver">[1]</a>, <a href="moose_classes.html#MarkovGslSolver">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable">MarkovRateTable (built-in class)</a>, <a href="moose_builtins.html#MarkovRateTable">[1]</a>, <a href="moose_classes.html#MarkovRateTable">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolver">MarkovSolver (built-in class)</a>, <a href="moose_builtins.html#MarkovSolver">[1]</a>, <a href="moose_classes.html#MarkovSolver">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase">MarkovSolverBase (built-in class)</a>, <a href="moose_builtins.html#MarkovSolverBase">[1]</a>, <a href="moose_classes.html#MarkovSolverBase">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MathFunc">MathFunc (built-in class)</a>, <a href="moose_builtins.html#MathFunc">[1]</a>, <a href="moose_classes.html#MathFunc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MathFunc.mathML">mathML (MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.mathML">[1]</a>, <a href="moose_classes.html#MathFunc.mathML">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.matrixEntry">matrixEntry (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.matrixEntry">[1]</a>, <a href="moose_classes.html#Stoich.matrixEntry">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.max">max (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.max">[1]</a>, <a href="moose_classes.html#HHGate.max">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.maxIter">maxIter (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.maxIter">[1]</a>, <a href="moose_classes.html#SteadyState.maxIter">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.me">me (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.me">[1]</a>, <a href="moose_classes.html#Neutral.me">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats.mean">mean (Stats attribute)</a>, <a href="moose_builtins.html#Stats.mean">[1]</a>, <a href="moose_classes.html#Stats.mean">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.mesh">mesh (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.mesh">[1]</a>, <a href="moose_classes.html#MeshEntry.mesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry">MeshEntry (built-in class)</a>, <a href="moose_builtins.html#MeshEntry">[1]</a>, <a href="moose_classes.html#MeshEntry">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.meshToSpace">meshToSpace (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.meshToSpace">[1]</a>, <a href="moose_classes.html#CubeMesh.meshToSpace">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.meshType">meshType (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.meshType">[1]</a>, <a href="moose_classes.html#MeshEntry.meshType">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#method">method</a>, <a href="moose_builtins.html#method">[1]</a>, <a href="moose_classes.html#method">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Ksolve.method">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.method">[1]</a>, <a href="moose_classes.html#Ksolve.method">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.method">(MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.method">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.method">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MgBlock">MgBlock (built-in class)</a>, <a href="moose_builtins.html#MgBlock">[1]</a>, <a href="moose_classes.html#MgBlock">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#HHGate.min">min (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.min">[1]</a>, <a href="moose_classes.html#HHGate.min">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.mInfinity">mInfinity (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.mInfinity">[1]</a>, <a href="moose_classes.html#HHGate.mInfinity">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.minusIn">minusIn() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.minusIn">[1]</a>, <a href="moose_classes.html#DiffAmp.minusIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MMenz">MMenz (built-in class)</a>, <a href="moose_builtins.html#MMenz">[1]</a>, <a href="moose_classes.html#MMenz">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#mmPump">mmPump()</a>, <a href="moose_builtins.html#mmPump">[1]</a>, <a href="moose_classes.html#mmPump">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#mode">mode</a>, <a href="moose_builtins.html#mode">[1]</a>, <a href="moose_classes.html#mode">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VClamp.mode">(VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.mode">[1]</a>, <a href="moose_classes.html#VClamp.mode">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SynChan.modulator">modulator() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.modulator">[1]</a>, <a href="moose_classes.html#SynChan.modulator">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Species.molWt">molWt (Species attribute)</a>, <a href="moose_builtins.html#Species.molWt">[1]</a>, <a href="moose_classes.html#Species.molWt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Species.molWtOut">molWtOut (Species attribute)</a>, <a href="moose_builtins.html#Species.molWtOut">[1]</a>, <a href="moose_classes.html#Species.molWtOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.motorConst">motorConst (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.motorConst">[1]</a>, <a href="moose_classes.html#PoolBase.motorConst">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Shell.move">move() (Shell method)</a>, <a href="moose_builtins.html#Shell.move">[1]</a>, <a href="moose_classes.html#Shell.move">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg">Msg (built-in class)</a>, <a href="moose_builtins.html#Msg">[1]</a>, <a href="moose_classes.html#Msg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.msgDestFunctions">msgDestFunctions (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.msgDestFunctions">[1]</a>, <a href="moose_classes.html#Neutral.msgDestFunctions">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.msgDests">msgDests (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.msgDests">[1]</a>, <a href="moose_classes.html#Neutral.msgDests">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.msgIn">msgIn (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.msgIn">[1]</a>, <a href="moose_classes.html#Neutral.msgIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.msgOut">msgOut (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.msgOut">[1]</a>, <a href="moose_classes.html#Neutral.msgOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Mstring">Mstring (built-in class)</a>, <a href="moose_builtins.html#Mstring">[1]</a>, <a href="moose_classes.html#Mstring">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PostMaster.myNode">myNode (PostMaster attribute)</a>, <a href="moose_builtins.html#PostMaster.myNode">[1]</a>, <a href="moose_classes.html#PostMaster.myNode">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="N">N</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#PoolBase.n">n (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.n">[1]</a>, <a href="moose_classes.html#PoolBase.n">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.name">name (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.name">[1]</a>, <a href="moose_classes.html#Neutral.name">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.neighbors">neighbors (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.neighbors">[1]</a>, <a href="moose_classes.html#MeshEntry.neighbors">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Neutral.neighbors">(Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.neighbors">[1]</a>, <a href="moose_classes.html#Neutral.neighbors">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Nernst">Nernst (built-in class)</a>, <a href="moose_builtins.html#Nernst">[1]</a>, <a href="moose_classes.html#Nernst">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh">NeuroMesh (built-in class)</a>, <a href="moose_builtins.html#NeuroMesh">[1]</a>, <a href="moose_classes.html#NeuroMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neuron">Neuron (built-in class)</a>, <a href="moose_builtins.html#Neuron">[1]</a>, <a href="moose_classes.html#Neuron">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral">Neutral (built-in class)</a>, <a href="moose_builtins.html#Neutral">[1]</a>, <a href="moose_classes.html#Neutral">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.nInit">nInit (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.nInit">[1]</a>, <a href="moose_classes.html#PoolBase.nInit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.nIter">nIter (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.nIter">[1]</a>, <a href="moose_classes.html#SteadyState.nIter">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.nNegEigenvalues">nNegEigenvalues (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.nNegEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.nNegEigenvalues">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.normalizeWeights">normalizeWeights (SynChan attribute)</a>, <a href="moose_builtins.html#SynChan.normalizeWeights">[1]</a>, <a href="moose_classes.html#SynChan.normalizeWeights">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.notes">notes (Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.notes">[1]</a>, <a href="moose_classes.html#Annotator.notes">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.nOut">nOut (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.nOut">[1]</a>, <a href="moose_classes.html#PoolBase.nOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.nPosEigenvalues">nPosEigenvalues (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.nPosEigenvalues">[1]</a>, <a href="moose_classes.html#SteadyState.nPosEigenvalues">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.nsteps">nsteps (Clock attribute)</a>, <a href="moose_builtins.html#Clock.nsteps">[1]</a>, <a href="moose_classes.html#Clock.nsteps">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats.num">num (Stats attribute)</a>, <a href="moose_builtins.html#Stats.num">[1]</a>, <a href="moose_classes.html#Stats.num">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.numAllPools">numAllPools (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.numAllPools">[1]</a>, <a href="moose_classes.html#Stoich.numAllPools">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.numAllVoxels">numAllVoxels (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.numAllVoxels">[1]</a>, <a href="moose_classes.html#Dsolve.numAllVoxels">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.numAllVoxels">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.numAllVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.numAllVoxels">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.numAllVoxels">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.numAllVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.numAllVoxels">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SparseMsg.numColumns">numColumns (SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.numColumns">[1]</a>, <a href="moose_classes.html#SparseMsg.numColumns">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.numData">numData (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.numData">[1]</a>, <a href="moose_classes.html#Neutral.numData">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.numDiffCompts">numDiffCompts (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.numDiffCompts">[1]</a>, <a href="moose_classes.html#CylMesh.numDiffCompts">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#NeuroMesh.numDiffCompts">(NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.numDiffCompts">[1]</a>, <a href="moose_classes.html#NeuroMesh.numDiffCompts">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChemCompt.numDimensions">numDimensions (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.numDimensions">[1]</a>, <a href="moose_classes.html#ChemCompt.numDimensions">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.numEntries">numEntries (SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.numEntries">[1]</a>, <a href="moose_classes.html#SparseMsg.numEntries">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Neutral.numField">numField (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.numField">[1]</a>, <a href="moose_classes.html#Neutral.numField">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.numKb">numKb (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.numKb">[1]</a>, <a href="moose_classes.html#ReacBase.numKb">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.numKf">numKf (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.numKf">[1]</a>, <a href="moose_classes.html#ReacBase.numKf">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.numKm">numKm (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.numKm">[1]</a>, <a href="moose_classes.html#EnzBase.numKm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve.numLocalVoxels">numLocalVoxels (Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.numLocalVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.numLocalVoxels">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Ksolve.numLocalVoxels">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.numLocalVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.numLocalVoxels">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PostMaster.numNodes">numNodes (PostMaster attribute)</a>, <a href="moose_builtins.html#PostMaster.numNodes">[1]</a>, <a href="moose_classes.html#PostMaster.numNodes">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.numOpenStates">numOpenStates (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.numOpenStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.numOpenStates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.numPools">numPools (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.numPools">[1]</a>, <a href="moose_classes.html#Dsolve.numPools">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.numPools">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.numPools">[1]</a>, <a href="moose_classes.html#Gsolve.numPools">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.numPools">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.numPools">[1]</a>, <a href="moose_classes.html#Ksolve.numPools">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ReacBase.numProducts">numProducts (ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.numProducts">[1]</a>, <a href="moose_classes.html#ReacBase.numProducts">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.numRates">numRates (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.numRates">[1]</a>, <a href="moose_classes.html#Stoich.numRates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.numRows">numRows (SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.numRows">[1]</a>, <a href="moose_classes.html#SparseMsg.numRows">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh.numSegments">numSegments (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.numSegments">[1]</a>, <a href="moose_classes.html#NeuroMesh.numSegments">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.numStates">numStates (MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.numStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.numStates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.numSubstrates">numSubstrates (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.numSubstrates">[1]</a>, <a href="moose_classes.html#EnzBase.numSubstrates">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ReacBase.numSubstrates">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.numSubstrates">[1]</a>, <a href="moose_classes.html#ReacBase.numSubstrates">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SynHandler.numSynapses">numSynapses (SynHandler attribute)</a>, <a href="moose_builtins.html#SynHandler.numSynapses">[1]</a>, <a href="moose_classes.html#SynHandler.numSynapses">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.numTicks">numTicks (Clock attribute)</a>, <a href="moose_builtins.html#Clock.numTicks">[1]</a>, <a href="moose_classes.html#Clock.numTicks">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.numVarPools">numVarPools (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.numVarPools">[1]</a>, <a href="moose_classes.html#SteadyState.numVarPools">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Stoich.numVarPools">(Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.numVarPools">[1]</a>, <a href="moose_classes.html#Stoich.numVarPools">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Dsolve.numVoxels">numVoxels (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.numVoxels">[1]</a>, <a href="moose_classes.html#Dsolve.numVoxels">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.nVec">nVec (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.nVec">[1]</a>, <a href="moose_classes.html#Dsolve.nVec">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.nVec">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.nVec">[1]</a>, <a href="moose_classes.html#Gsolve.nVec">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.nVec">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.nVec">[1]</a>, <a href="moose_classes.html#Ksolve.nVec">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.nx">nx (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.nx">[1]</a>, <a href="moose_classes.html#CubeMesh.nx">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.ny">ny (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.ny">[1]</a>, <a href="moose_classes.html#CubeMesh.ny">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.nz">nz (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.nz">[1]</a>, <a href="moose_classes.html#CubeMesh.nz">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="O">O</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#OneToAllMsg">OneToAllMsg (built-in class)</a>, <a href="moose_builtins.html#OneToAllMsg">[1]</a>, <a href="moose_classes.html#OneToAllMsg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#OneToOneDataIndexMsg">OneToOneDataIndexMsg (built-in class)</a>, <a href="moose_builtins.html#OneToOneDataIndexMsg">[1]</a>, <a href="moose_classes.html#OneToOneDataIndexMsg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#OneToOneMsg">OneToOneMsg (built-in class)</a>, <a href="moose_builtins.html#OneToOneMsg">[1]</a>, <a href="moose_classes.html#OneToOneMsg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChemCompt.oneVoxelVolume">oneVoxelVolume (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.oneVoxelVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.oneVoxelVolume">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.origChannel">origChannel() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.origChannel">[1]</a>, <a href="moose_classes.html#MgBlock.origChannel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#outerArea">outerArea</a>, <a href="moose_builtins.html#outerArea">[1]</a>, <a href="moose_classes.html#outerArea">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#outerDif">outerDif</a>, <a href="moose_builtins.html#outerDif">[1]</a>, <a href="moose_classes.html#outerDif">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#outerDifSourceOut">outerDifSourceOut</a>, <a href="moose_builtins.html#outerDifSourceOut">[1]</a>, <a href="moose_classes.html#outerDifSourceOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#outflux">outflux()</a>, <a href="moose_builtins.html#outflux">[1]</a>, <a href="moose_classes.html#outflux">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.output">output (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.output">[1]</a>, <a href="moose_classes.html#Adaptor.output">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Arith.output">(Arith attribute)</a>, <a href="moose_builtins.html#Arith.output">[1]</a>, <a href="moose_classes.html#Arith.output">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.output">(DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.output">[1]</a>, <a href="moose_classes.html#DiffAmp.output">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#FuncBase.output">(FuncBase attribute)</a>, <a href="moose_builtins.html#FuncBase.output">[1]</a>, <a href="moose_classes.html#FuncBase.output">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MathFunc.output">(MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.output">[1]</a>, <a href="moose_classes.html#MathFunc.output">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.output">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.output">[1]</a>, <a href="moose_classes.html#PIDController.output">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.output">(PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.output">[1]</a>, <a href="moose_classes.html#PulseGen.output">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.output">(RC attribute)</a>, <a href="moose_builtins.html#RC.output">[1]</a>, <a href="moose_classes.html#RC.output">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.output">(StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.output">[1]</a>, <a href="moose_classes.html#StimulusTable.output">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Adaptor.outputOffset">outputOffset (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.outputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.outputOffset">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.outputValue">outputValue (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.outputValue">[1]</a>, <a href="moose_classes.html#Adaptor.outputValue">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Arith.outputValue">(Arith attribute)</a>, <a href="moose_builtins.html#Arith.outputValue">[1]</a>, <a href="moose_classes.html#Arith.outputValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.outputValue">(DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.outputValue">[1]</a>, <a href="moose_classes.html#DiffAmp.outputValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.outputValue">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.outputValue">[1]</a>, <a href="moose_classes.html#PIDController.outputValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.outputValue">(PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.outputValue">[1]</a>, <a href="moose_classes.html#PulseGen.outputValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.outputValue">(TableBase attribute)</a>, <a href="moose_builtins.html#TableBase.outputValue">[1]</a>, <a href="moose_classes.html#TableBase.outputValue">[2]</a>
- </dt>
-
- </dl></dd>
- </dl></td>
-</tr></table>
-
-<h2 id="P">P</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#SparseMsg.pairFill">pairFill() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.pairFill">[1]</a>, <a href="moose_classes.html#SparseMsg.pairFill">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.parent">parent (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.parent">[1]</a>, <a href="moose_classes.html#Neutral.parent">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.parentMsg">parentMsg() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.parentMsg">[1]</a>, <a href="moose_classes.html#Neutral.parentMsg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh.parentVoxel">parentVoxel (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.parentVoxel">[1]</a>, <a href="moose_classes.html#NeuroMesh.parentVoxel">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SpineMesh.parentVoxel">(SpineMesh attribute)</a>, <a href="moose_builtins.html#SpineMesh.parentVoxel">[1]</a>, <a href="moose_classes.html#SpineMesh.parentVoxel">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Dsolve.path">path (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.path">[1]</a>, <a href="moose_classes.html#Dsolve.path">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Neutral.path">(Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.path">[1]</a>, <a href="moose_classes.html#Neutral.path">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.path">(Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.path">[1]</a>, <a href="moose_classes.html#Stoich.path">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChanBase.permeabilityOut">permeabilityOut (ChanBase attribute)</a>, <a href="moose_builtins.html#ChanBase.permeabilityOut">[1]</a>, <a href="moose_classes.html#ChanBase.permeabilityOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.permeabilityOut">(SynChanBase attribute)</a>, <a href="moose_builtins.html#SynChanBase.permeabilityOut">[1]</a>, <a href="moose_classes.html#SynChanBase.permeabilityOut">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PIDController">PIDController (built-in class)</a>, <a href="moose_builtins.html#PIDController">[1]</a>, <a href="moose_classes.html#PIDController">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.plainPlot">plainPlot() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.plainPlot">[1]</a>, <a href="moose_classes.html#TableBase.plainPlot">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.plusIn">plusIn() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.plusIn">[1]</a>, <a href="moose_classes.html#DiffAmp.plusIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Pool">Pool (built-in class)</a>, <a href="moose_builtins.html#Pool">[1]</a>, <a href="moose_classes.html#Pool">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Species.pool">pool (Species attribute)</a>, <a href="moose_builtins.html#Species.pool">[1]</a>, <a href="moose_classes.html#Species.pool">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase">PoolBase (built-in class)</a>, <a href="moose_builtins.html#PoolBase">[1]</a>, <a href="moose_classes.html#PoolBase">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.poolIdMap">poolIdMap (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.poolIdMap">[1]</a>, <a href="moose_classes.html#Stoich.poolIdMap">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PostMaster">PostMaster (built-in class)</a>, <a href="moose_builtins.html#PostMaster">[1]</a>, <a href="moose_classes.html#PostMaster">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.prd">prd (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.prd">[1]</a>, <a href="moose_classes.html#EnzBase.prd">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ReacBase.prd">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.prd">[1]</a>, <a href="moose_classes.html#ReacBase.prd">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#EnzBase.prdDest">prdDest() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.prdDest">[1]</a>, <a href="moose_classes.html#EnzBase.prdDest">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ReacBase.prdDest">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.prdDest">[1]</a>, <a href="moose_classes.html#ReacBase.prdDest">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#EnzBase.prdOut">prdOut (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.prdOut">[1]</a>, <a href="moose_classes.html#EnzBase.prdOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ReacBase.prdOut">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.prdOut">[1]</a>, <a href="moose_classes.html#ReacBase.prdOut">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.preserveNumEntries">preserveNumEntries (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.preserveNumEntries">[1]</a>, <a href="moose_classes.html#CubeMesh.preserveNumEntries">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.probability">probability (SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.probability">[1]</a>, <a href="moose_classes.html#SparseMsg.probability">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#proc">proc</a>, <a href="moose_builtins.html#proc">[1]</a>, <a href="moose_classes.html#proc">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Adaptor.proc">(Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.proc">[1]</a>, <a href="moose_classes.html#Adaptor.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.proc">(Arith attribute)</a>, <a href="moose_builtins.html#Arith.proc">[1]</a>, <a href="moose_classes.html#Arith.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#BufPool.proc">(BufPool attribute)</a>, <a href="moose_builtins.html#BufPool.proc">[1]</a>, <a href="moose_classes.html#BufPool.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.proc">(CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.proc">[1]</a>, <a href="moose_classes.html#CaConc.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.proc">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.proc">[1]</a>, <a href="moose_classes.html#CompartmentBase.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.proc">(DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.proc">[1]</a>, <a href="moose_classes.html#DiffAmp.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.proc">(Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.proc">[1]</a>, <a href="moose_classes.html#Dsolve.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.proc">(EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.proc">[1]</a>, <a href="moose_classes.html#EnzBase.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.proc">(Func attribute)</a>, <a href="moose_builtins.html#Func.proc">[1]</a>, <a href="moose_classes.html#Func.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#FuncBase.proc">(FuncBase attribute)</a>, <a href="moose_builtins.html#FuncBase.proc">[1]</a>, <a href="moose_classes.html#FuncBase.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve.proc">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.proc">[1]</a>, <a href="moose_classes.html#Gsolve.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.proc">(HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.proc">[1]</a>, <a href="moose_classes.html#HHChannel.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.proc">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.proc">[1]</a>, <a href="moose_classes.html#HHChannel2D.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.proc">(HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.proc">[1]</a>, <a href="moose_classes.html#HSolve.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.proc">(IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.proc">[1]</a>, <a href="moose_classes.html#IntFire.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.proc">(Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.proc">[1]</a>, <a href="moose_classes.html#Interpol.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.proc">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.proc">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.proc">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.proc">[1]</a>, <a href="moose_classes.html#Ksolve.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Leakage.proc">(Leakage attribute)</a>, <a href="moose_builtins.html#Leakage.proc">[1]</a>, <a href="moose_classes.html#Leakage.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.proc">(MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.proc">[1]</a>, <a href="moose_classes.html#MarkovChannel.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.proc">(MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.proc">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.proc">(MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.proc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolver.proc">(MarkovSolver attribute)</a>, <a href="moose_builtins.html#MarkovSolver.proc">[1]</a>, <a href="moose_classes.html#MarkovSolver.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.proc">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.proc">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MathFunc.proc">(MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.proc">[1]</a>, <a href="moose_classes.html#MathFunc.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.proc">(MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.proc">[1]</a>, <a href="moose_classes.html#MeshEntry.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.proc">(MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.proc">[1]</a>, <a href="moose_classes.html#MgBlock.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.proc">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.proc">[1]</a>, <a href="moose_classes.html#PIDController.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.proc">(PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.proc">[1]</a>, <a href="moose_classes.html#PoolBase.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PostMaster.proc">(PostMaster attribute)</a>, <a href="moose_builtins.html#PostMaster.proc">[1]</a>, <a href="moose_classes.html#PostMaster.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.proc">(PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.proc">[1]</a>, <a href="moose_classes.html#PulseGen.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.proc">(RC attribute)</a>, <a href="moose_builtins.html#RC.proc">[1]</a>, <a href="moose_classes.html#RC.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.proc">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.proc">[1]</a>, <a href="moose_classes.html#ReacBase.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.proc">(SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.proc">[1]</a>, <a href="moose_classes.html#SpikeGen.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats.proc">(Stats attribute)</a>, <a href="moose_builtins.html#Stats.proc">[1]</a>, <a href="moose_classes.html#Stats.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.proc">(StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.proc">[1]</a>, <a href="moose_classes.html#StimulusTable.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.proc">(SynChan attribute)</a>, <a href="moose_builtins.html#SynChan.proc">[1]</a>, <a href="moose_classes.html#SynChan.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Table.proc">(Table attribute)</a>, <a href="moose_builtins.html#Table.proc">[1]</a>, <a href="moose_classes.html#Table.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.proc">(TimeTable attribute)</a>, <a href="moose_builtins.html#TimeTable.proc">[1]</a>, <a href="moose_classes.html#TimeTable.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.proc">(VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.proc">[1]</a>, <a href="moose_classes.html#VClamp.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCaConc.proc">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.proc">[1]</a>, <a href="moose_classes.html#ZombieCaConc.proc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.proc">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.proc">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.proc">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.proc0">proc0 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc0">[1]</a>, <a href="moose_classes.html#Clock.proc0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.proc1">proc1 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc1">[1]</a>, <a href="moose_classes.html#Clock.proc1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.proc2">proc2 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc2">[1]</a>, <a href="moose_classes.html#Clock.proc2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.proc3">proc3 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc3">[1]</a>, <a href="moose_classes.html#Clock.proc3">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.proc4">proc4 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc4">[1]</a>, <a href="moose_classes.html#Clock.proc4">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Clock.proc5">proc5 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc5">[1]</a>, <a href="moose_classes.html#Clock.proc5">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.proc6">proc6 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc6">[1]</a>, <a href="moose_classes.html#Clock.proc6">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.proc7">proc7 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc7">[1]</a>, <a href="moose_classes.html#Clock.proc7">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.proc8">proc8 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc8">[1]</a>, <a href="moose_classes.html#Clock.proc8">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.proc9">proc9 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.proc9">[1]</a>, <a href="moose_classes.html#Clock.proc9">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#process">process()</a>, <a href="tmp.html#process">[1]</a>, <a href="tmp.html#process">[2]</a>, <a href="tmp.html#process">[3]</a>, <a href="tmp.html#process">[4]</a>, <a href="moose_builtins.html#process">[5]</a>, <a href="moose_builtins.html#process">[6]</a>, <a href="moose_builtins.html#process">[7]</a>, <a href="moose_builtins.html#process">[8]</a>, <a href="moose_builtins.html#process">[9]</a>, <a href="moose_classes.html#process">[10]</a>, <a href="moose_classes.html#process">[11]</a>, <a href="moose_classes.html#process">[12]</a>, <a href="moose_classes.html#process">[13]</a>, <a href="moose_classes.html#process">[14]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Adaptor.process">(Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.process">[1]</a>, <a href="moose_classes.html#Adaptor.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.process">(Arith method)</a>, <a href="moose_builtins.html#Arith.process">[1]</a>, <a href="moose_classes.html#Arith.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#BufPool.process">(BufPool method)</a>, <a href="moose_builtins.html#BufPool.process">[1]</a>, <a href="moose_classes.html#BufPool.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.process">(CaConc method)</a>, <a href="moose_builtins.html#CaConc.process">[1]</a>, <a href="moose_classes.html#CaConc.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.process">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.process">[1]</a>, <a href="moose_classes.html#CompartmentBase.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.process">(DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.process">[1]</a>, <a href="moose_classes.html#DiffAmp.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.process">(Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.process">[1]</a>, <a href="moose_classes.html#Dsolve.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.process">(EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.process">[1]</a>, <a href="moose_classes.html#EnzBase.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#FuncBase.process">(FuncBase method)</a>, <a href="moose_builtins.html#FuncBase.process">[1]</a>, <a href="moose_classes.html#FuncBase.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve.process">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.process">[1]</a>, <a href="moose_classes.html#Gsolve.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.process">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.process">[1]</a>, <a href="moose_classes.html#HHChannel.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.process">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.process">[1]</a>, <a href="moose_classes.html#HHChannel2D.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.process">(HSolve method)</a>, <a href="moose_builtins.html#HSolve.process">[1]</a>, <a href="moose_classes.html#HSolve.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.process">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.process">[1]</a>, <a href="moose_classes.html#IntFire.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.process">(Interpol method)</a>, <a href="moose_builtins.html#Interpol.process">[1]</a>, <a href="moose_classes.html#Interpol.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.process">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.process">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.process">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.process">[1]</a>, <a href="moose_classes.html#Ksolve.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.process">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.process">[1]</a>, <a href="moose_classes.html#MarkovChannel.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.process">(MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.process">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.process">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.process">[1]</a>, <a href="moose_classes.html#MarkovRateTable.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolver.process">(MarkovSolver method)</a>, <a href="moose_builtins.html#MarkovSolver.process">[1]</a>, <a href="moose_classes.html#MarkovSolver.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.process">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.process">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MathFunc.process">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.process">[1]</a>, <a href="moose_classes.html#MathFunc.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.process">(MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.process">[1]</a>, <a href="moose_classes.html#MeshEntry.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.process">(MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.process">[1]</a>, <a href="moose_classes.html#MgBlock.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.process">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.process">[1]</a>, <a href="moose_classes.html#PIDController.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.process">(PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.process">[1]</a>, <a href="moose_classes.html#PoolBase.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PostMaster.process">(PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.process">[1]</a>, <a href="moose_classes.html#PostMaster.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.process">(PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.process">[1]</a>, <a href="moose_classes.html#PulseGen.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.process">(RC method)</a>, <a href="moose_builtins.html#RC.process">[1]</a>, <a href="moose_classes.html#RC.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.process">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.process">[1]</a>, <a href="moose_classes.html#ReacBase.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.process">(SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.process">[1]</a>, <a href="moose_classes.html#SpikeGen.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats.process">(Stats method)</a>, <a href="tmp.html#Stats.process">[1]</a>, <a href="moose_builtins.html#Stats.process">[2]</a>, <a href="moose_builtins.html#Stats.process">[3]</a>, <a href="moose_classes.html#Stats.process">[4]</a>, <a href="moose_classes.html#Stats.process">[5]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.process">(StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.process">[1]</a>, <a href="moose_classes.html#StimulusTable.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.process">(SynChan method)</a>, <a href="moose_builtins.html#SynChan.process">[1]</a>, <a href="moose_classes.html#SynChan.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Table.process">(Table method)</a>, <a href="moose_builtins.html#Table.process">[1]</a>, <a href="moose_classes.html#Table.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.process">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.process">[1]</a>, <a href="moose_classes.html#TimeTable.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.process">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.process">[1]</a>, <a href="moose_classes.html#VClamp.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCaConc.process">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.process">[1]</a>, <a href="moose_classes.html#ZombieCaConc.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.process">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.process">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.process">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#testSched.process">(testSched method)</a>, <a href="moose_builtins.html#testSched.process">[1]</a>, <a href="moose_classes.html#testSched.process">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.process0">process0 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process0">[1]</a>, <a href="moose_classes.html#Clock.process0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.process1">process1 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process1">[1]</a>, <a href="moose_classes.html#Clock.process1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.process2">process2 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process2">[1]</a>, <a href="moose_classes.html#Clock.process2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.process3">process3 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process3">[1]</a>, <a href="moose_classes.html#Clock.process3">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.process4">process4 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process4">[1]</a>, <a href="moose_classes.html#Clock.process4">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.process5">process5 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process5">[1]</a>, <a href="moose_classes.html#Clock.process5">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.process6">process6 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process6">[1]</a>, <a href="moose_classes.html#Clock.process6">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.process7">process7 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process7">[1]</a>, <a href="moose_classes.html#Clock.process7">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.process8">process8 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process8">[1]</a>, <a href="moose_classes.html#Clock.process8">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.process9">process9 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.process9">[1]</a>, <a href="moose_classes.html#Clock.process9">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DifShell.process_0">process_0 (DifShell attribute)</a>, <a href="moose_builtins.html#DifShell.process_0">[1]</a>, <a href="moose_classes.html#DifShell.process_0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DifShell.process_1">process_1 (DifShell attribute)</a>, <a href="moose_builtins.html#DifShell.process_1">[1]</a>, <a href="moose_classes.html#DifShell.process_1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SymCompartment.proximal">proximal (SymCompartment attribute)</a>, <a href="moose_builtins.html#SymCompartment.proximal">[1]</a>, <a href="moose_classes.html#SymCompartment.proximal">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#proximalOnly">proximalOnly</a>, <a href="moose_builtins.html#proximalOnly">[1]</a>, <a href="moose_classes.html#proximalOnly">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#proximalOut">proximalOut</a>, <a href="tmp.html#proximalOut">[1]</a>, <a href="moose_builtins.html#proximalOut">[2]</a>, <a href="moose_builtins.html#proximalOut">[3]</a>, <a href="moose_classes.html#proximalOut">[4]</a>, <a href="moose_classes.html#proximalOut">[5]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PsdMesh.psdList">psdList() (PsdMesh method)</a>, <a href="moose_builtins.html#PsdMesh.psdList">[1]</a>, <a href="moose_classes.html#PsdMesh.psdList">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh.psdListOut">psdListOut (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.psdListOut">[1]</a>, <a href="moose_classes.html#NeuroMesh.psdListOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PsdMesh">PsdMesh (built-in class)</a>, <a href="moose_builtins.html#PsdMesh">[1]</a>, <a href="moose_classes.html#PsdMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen">PulseGen (built-in class)</a>, <a href="moose_builtins.html#PulseGen">[1]</a>, <a href="moose_classes.html#PulseGen">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="Q">Q</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#MarkovRateTable.Q">Q (MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.Q">[1]</a>, <a href="moose_classes.html#MarkovRateTable.Q">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.Q">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.Q">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.Q">[2]</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Shell.quit">quit() (Shell method)</a>, <a href="moose_builtins.html#Shell.quit">[1]</a>, <a href="moose_classes.html#Shell.quit">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="R">R</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#RC.R">R (RC attribute)</a>, <a href="moose_builtins.html#RC.R">[1]</a>, <a href="moose_classes.html#RC.R">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.r0">r0 (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.r0">[1]</a>, <a href="moose_classes.html#CylMesh.r0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.r1">r1 (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.r1">[1]</a>, <a href="moose_classes.html#CylMesh.r1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.Ra">Ra (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Ra">[1]</a>, <a href="moose_classes.html#CompartmentBase.Ra">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.randInject">randInject() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.randInject">[1]</a>, <a href="moose_classes.html#CompartmentBase.randInject">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.randomInit">randomInit() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.randomInit">[1]</a>, <a href="moose_classes.html#SteadyState.randomInit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.rank">rank (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.rank">[1]</a>, <a href="moose_classes.html#SteadyState.rank">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.ratio">ratio (CplxEnzBase attribute)</a>, <a href="moose_builtins.html#CplxEnzBase.ratio">[1]</a>, <a href="moose_classes.html#CplxEnzBase.ratio">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.raxial">raxial (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.raxial">[1]</a>, <a href="moose_classes.html#CompartmentBase.raxial">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#raxialCylinder">raxialCylinder()</a>, <a href="moose_builtins.html#raxialCylinder">[1]</a>, <a href="moose_classes.html#raxialCylinder">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.raxialOut">raxialOut (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.raxialOut">[1]</a>, <a href="moose_classes.html#CompartmentBase.raxialOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#raxialSphere">raxialSphere()</a>, <a href="tmp.html#raxialSphere">[1]</a>, <a href="moose_builtins.html#raxialSphere">[2]</a>, <a href="moose_builtins.html#raxialSphere">[3]</a>, <a href="moose_classes.html#raxialSphere">[4]</a>, <a href="moose_classes.html#raxialSphere">[5]</a>
- </dt>
-
-
- <dt><a href="tmp.html#raxialSym">raxialSym()</a>, <a href="tmp.html#raxialSym">[1]</a>, <a href="tmp.html#raxialSym">[2]</a>, <a href="moose_builtins.html#raxialSym">[3]</a>, <a href="moose_builtins.html#raxialSym">[4]</a>, <a href="moose_builtins.html#raxialSym">[5]</a>, <a href="moose_classes.html#raxialSym">[6]</a>, <a href="moose_classes.html#raxialSym">[7]</a>, <a href="moose_classes.html#raxialSym">[8]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC">RC (built-in class)</a>, <a href="moose_builtins.html#RC">[1]</a>, <a href="moose_classes.html#RC">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Reac">Reac (built-in class)</a>, <a href="moose_builtins.html#Reac">[1]</a>, <a href="moose_classes.html#Reac">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.reac">reac (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.reac">[1]</a>, <a href="moose_classes.html#PoolBase.reac">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase">ReacBase (built-in class)</a>, <a href="moose_builtins.html#ReacBase">[1]</a>, <a href="moose_classes.html#ReacBase">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.reacDest">reacDest() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.reacDest">[1]</a>, <a href="moose_classes.html#PoolBase.reacDest">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#reaction">reaction()</a>, <a href="moose_builtins.html#reaction">[1]</a>, <a href="moose_classes.html#reaction">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.refractoryPeriod">refractoryPeriod (IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.refractoryPeriod">[1]</a>, <a href="moose_classes.html#IntFire.refractoryPeriod">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.refractT">refractT (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.refractT">[1]</a>, <a href="moose_classes.html#SpikeGen.refractT">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#reinit">reinit()</a>, <a href="tmp.html#reinit">[1]</a>, <a href="tmp.html#reinit">[2]</a>, <a href="tmp.html#reinit">[3]</a>, <a href="tmp.html#reinit">[4]</a>, <a href="moose_builtins.html#reinit">[5]</a>, <a href="moose_builtins.html#reinit">[6]</a>, <a href="moose_builtins.html#reinit">[7]</a>, <a href="moose_builtins.html#reinit">[8]</a>, <a href="moose_builtins.html#reinit">[9]</a>, <a href="moose_classes.html#reinit">[10]</a>, <a href="moose_classes.html#reinit">[11]</a>, <a href="moose_classes.html#reinit">[12]</a>, <a href="moose_classes.html#reinit">[13]</a>, <a href="moose_classes.html#reinit">[14]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Adaptor.reinit">(Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.reinit">[1]</a>, <a href="moose_classes.html#Adaptor.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.reinit">(Arith method)</a>, <a href="moose_builtins.html#Arith.reinit">[1]</a>, <a href="moose_classes.html#Arith.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#BufPool.reinit">(BufPool method)</a>, <a href="moose_builtins.html#BufPool.reinit">[1]</a>, <a href="moose_classes.html#BufPool.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.reinit">(CaConc method)</a>, <a href="moose_builtins.html#CaConc.reinit">[1]</a>, <a href="moose_classes.html#CaConc.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.reinit">(Clock method)</a>, <a href="moose_builtins.html#Clock.reinit">[1]</a>, <a href="moose_classes.html#Clock.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.reinit">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.reinit">[1]</a>, <a href="moose_classes.html#CompartmentBase.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.reinit">(DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.reinit">[1]</a>, <a href="moose_classes.html#DiffAmp.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.reinit">(Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.reinit">[1]</a>, <a href="moose_classes.html#Dsolve.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.reinit">(EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.reinit">[1]</a>, <a href="moose_classes.html#EnzBase.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#FuncBase.reinit">(FuncBase method)</a>, <a href="moose_builtins.html#FuncBase.reinit">[1]</a>, <a href="moose_classes.html#FuncBase.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve.reinit">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.reinit">[1]</a>, <a href="moose_classes.html#Gsolve.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.reinit">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.reinit">[1]</a>, <a href="moose_classes.html#HHChannel.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.reinit">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.reinit">[1]</a>, <a href="moose_classes.html#HHChannel2D.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.reinit">(HSolve method)</a>, <a href="moose_builtins.html#HSolve.reinit">[1]</a>, <a href="moose_classes.html#HSolve.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.reinit">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.reinit">[1]</a>, <a href="moose_classes.html#IntFire.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.reinit">(Interpol method)</a>, <a href="moose_builtins.html#Interpol.reinit">[1]</a>, <a href="moose_classes.html#Interpol.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.reinit">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.reinit">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.reinit">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.reinit">[1]</a>, <a href="moose_classes.html#Ksolve.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.reinit">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.reinit">[1]</a>, <a href="moose_classes.html#MarkovChannel.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.reinit">(MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.reinit">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.reinit">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.reinit">[1]</a>, <a href="moose_classes.html#MarkovRateTable.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolver.reinit">(MarkovSolver method)</a>, <a href="moose_builtins.html#MarkovSolver.reinit">[1]</a>, <a href="moose_classes.html#MarkovSolver.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.reinit">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.reinit">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MathFunc.reinit">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.reinit">[1]</a>, <a href="moose_classes.html#MathFunc.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.reinit">(MeshEntry method)</a>, <a href="moose_builtins.html#MeshEntry.reinit">[1]</a>, <a href="moose_classes.html#MeshEntry.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.reinit">(MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.reinit">[1]</a>, <a href="moose_classes.html#MgBlock.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.reinit">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.reinit">[1]</a>, <a href="moose_classes.html#PIDController.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.reinit">(PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.reinit">[1]</a>, <a href="moose_classes.html#PoolBase.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PostMaster.reinit">(PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.reinit">[1]</a>, <a href="moose_classes.html#PostMaster.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.reinit">(PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.reinit">[1]</a>, <a href="moose_classes.html#PulseGen.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.reinit">(RC method)</a>, <a href="moose_builtins.html#RC.reinit">[1]</a>, <a href="moose_classes.html#RC.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.reinit">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.reinit">[1]</a>, <a href="moose_classes.html#ReacBase.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.reinit">(SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.reinit">[1]</a>, <a href="moose_classes.html#SpikeGen.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats.reinit">(Stats method)</a>, <a href="tmp.html#Stats.reinit">[1]</a>, <a href="moose_builtins.html#Stats.reinit">[2]</a>, <a href="moose_builtins.html#Stats.reinit">[3]</a>, <a href="moose_classes.html#Stats.reinit">[4]</a>, <a href="moose_classes.html#Stats.reinit">[5]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.reinit">(StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.reinit">[1]</a>, <a href="moose_classes.html#StimulusTable.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.reinit">(SynChan method)</a>, <a href="moose_builtins.html#SynChan.reinit">[1]</a>, <a href="moose_classes.html#SynChan.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Table.reinit">(Table method)</a>, <a href="moose_builtins.html#Table.reinit">[1]</a>, <a href="moose_classes.html#Table.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.reinit">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.reinit">[1]</a>, <a href="moose_classes.html#TimeTable.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.reinit">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.reinit">[1]</a>, <a href="moose_classes.html#VClamp.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCaConc.reinit">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.reinit">[1]</a>, <a href="moose_classes.html#ZombieCaConc.reinit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.reinit">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.reinit">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.reinit">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.reinit0">reinit0 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit0">[1]</a>, <a href="moose_classes.html#Clock.reinit0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.reinit1">reinit1 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit1">[1]</a>, <a href="moose_classes.html#Clock.reinit1">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Clock.reinit2">reinit2 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit2">[1]</a>, <a href="moose_classes.html#Clock.reinit2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.reinit3">reinit3 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit3">[1]</a>, <a href="moose_classes.html#Clock.reinit3">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.reinit4">reinit4 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit4">[1]</a>, <a href="moose_classes.html#Clock.reinit4">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.reinit5">reinit5 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit5">[1]</a>, <a href="moose_classes.html#Clock.reinit5">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.reinit6">reinit6 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit6">[1]</a>, <a href="moose_classes.html#Clock.reinit6">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.reinit7">reinit7 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit7">[1]</a>, <a href="moose_classes.html#Clock.reinit7">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.reinit8">reinit8 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit8">[1]</a>, <a href="moose_classes.html#Clock.reinit8">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.reinit9">reinit9 (Clock attribute)</a>, <a href="moose_builtins.html#Clock.reinit9">[1]</a>, <a href="moose_classes.html#Clock.reinit9">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.relativeAccuracy">relativeAccuracy (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.relativeAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.relativeAccuracy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.remesh">remesh() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.remesh">[1]</a>, <a href="moose_classes.html#EnzBase.remesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.remeshOut">remeshOut (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.remeshOut">[1]</a>, <a href="moose_classes.html#MeshEntry.remeshOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.remeshReacsOut">remeshReacsOut (MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.remeshReacsOut">[1]</a>, <a href="moose_classes.html#MeshEntry.remeshReacsOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.requestField">requestField (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.requestField">[1]</a>, <a href="moose_classes.html#Adaptor.requestField">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.requestInput">requestInput (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.requestInput">[1]</a>, <a href="moose_classes.html#Adaptor.requestInput">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.requestMolWt">requestMolWt (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.requestMolWt">[1]</a>, <a href="moose_classes.html#PoolBase.requestMolWt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Table.requestOut">requestOut (Table attribute)</a>, <a href="moose_builtins.html#Table.requestOut">[1]</a>, <a href="moose_classes.html#Table.requestOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChemCompt.resetStencil">resetStencil() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.resetStencil">[1]</a>, <a href="moose_classes.html#ChemCompt.resetStencil">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.resettle">resettle() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.resettle">[1]</a>, <a href="moose_classes.html#SteadyState.resettle">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#FuncBase.result">result (FuncBase attribute)</a>, <a href="moose_builtins.html#FuncBase.result">[1]</a>, <a href="moose_classes.html#FuncBase.result">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MathFunc.result">(MathFunc attribute)</a>, <a href="moose_builtins.html#MathFunc.result">[1]</a>, <a href="moose_classes.html#MathFunc.result">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.Rm">Rm (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Rm">[1]</a>, <a href="moose_classes.html#CompartmentBase.Rm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.RmByTau">RmByTau (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.RmByTau">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.RmByTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.rowStart">rowStart (Stoich attribute)</a>, <a href="moose_builtins.html#Stoich.rowStart">[1]</a>, <a href="moose_classes.html#Stoich.rowStart">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.runTime">runTime (Clock attribute)</a>, <a href="moose_builtins.html#Clock.runTime">[1]</a>, <a href="moose_classes.html#Clock.runTime">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="S">S</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#DiffAmp.saturation">saturation (DiffAmp attribute)</a>, <a href="moose_builtins.html#DiffAmp.saturation">[1]</a>, <a href="moose_classes.html#DiffAmp.saturation">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#PIDController.saturation">(PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.saturation">[1]</a>, <a href="moose_classes.html#PIDController.saturation">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Adaptor.scale">scale (Adaptor attribute)</a>, <a href="moose_builtins.html#Adaptor.scale">[1]</a>, <a href="moose_classes.html#Adaptor.scale">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Nernst.scale">(Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.scale">[1]</a>, <a href="moose_classes.html#Nernst.scale">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Stats.sdev">sdev (Stats attribute)</a>, <a href="moose_builtins.html#Stats.sdev">[1]</a>, <a href="moose_classes.html#Stats.sdev">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.secondDelay">secondDelay (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.secondDelay">[1]</a>, <a href="moose_classes.html#PulseGen.secondDelay">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.secondLevel">secondLevel (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.secondLevel">[1]</a>, <a href="moose_classes.html#PulseGen.secondLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.secondWidth">secondWidth (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.secondWidth">[1]</a>, <a href="moose_classes.html#PulseGen.secondWidth">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.seed">seed (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.seed">[1]</a>, <a href="moose_classes.html#HSolve.seed">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SparseMsg.seed">(SparseMsg attribute)</a>, <a href="moose_builtins.html#SparseMsg.seed">[1]</a>, <a href="moose_classes.html#SparseMsg.seed">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PIDController.sensed">sensed (PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.sensed">[1]</a>, <a href="moose_classes.html#PIDController.sensed">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VClamp.sensed">(VClamp attribute)</a>, <a href="moose_builtins.html#VClamp.sensed">[1]</a>, <a href="moose_classes.html#VClamp.sensed">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PIDController.sensedIn">sensedIn() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.sensedIn">[1]</a>, <a href="moose_classes.html#PIDController.sensedIn">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VClamp.sensedIn">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.sensedIn">[1]</a>, <a href="moose_classes.html#VClamp.sensedIn">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.separateSpines">separateSpines (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.separateSpines">[1]</a>, <a href="moose_classes.html#NeuroMesh.separateSpines">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.set1d">set1d() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.set1d">[1]</a>, <a href="moose_classes.html#MarkovRateTable.set1d">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.set2d">set2d() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.set2d">[1]</a>, <a href="moose_classes.html#MarkovRateTable.set2d">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.setA">setA() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setA">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.setAbs_refract">setAbs_refract() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.setAbs_refract">[1]</a>, <a href="moose_classes.html#SpikeGen.setAbs_refract">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.setAbsoluteAccuracy">setAbsoluteAccuracy() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.setAbsoluteAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.setAbsoluteAccuracy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.setAccommodating">setAccommodating() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setAccommodating">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setAccommodating">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.setAlpha">setAlpha() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setAlpha">[1]</a>, <a href="moose_classes.html#HHGate.setAlpha">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.setAlpha">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setAlpha">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setAlpha">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.setAlphaParms">setAlphaParms() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setAlphaParms">[1]</a>, <a href="moose_classes.html#HHGate.setAlphaParms">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.setAlwaysDiffuse">setAlwaysDiffuse() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setAlwaysDiffuse">[1]</a>, <a href="moose_classes.html#CubeMesh.setAlwaysDiffuse">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.setAnyValue">setAnyValue() (Arith method)</a>, <a href="moose_builtins.html#Arith.setAnyValue">[1]</a>, <a href="moose_classes.html#Arith.setAnyValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.setB">setB() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setB">[1]</a>, <a href="moose_classes.html#CaConc.setB">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.setB">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setB">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCaConc.setB">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setB">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setB">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.setBaseLevel">setBaseLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setBaseLevel">[1]</a>, <a href="moose_classes.html#PulseGen.setBaseLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.setBeta">setBeta() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setBeta">[1]</a>, <a href="moose_classes.html#HHGate.setBeta">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.setBeta">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setBeta">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setBeta">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PostMaster.setBufferSize">setBufferSize() (PostMaster method)</a>, <a href="moose_builtins.html#PostMaster.setBufferSize">[1]</a>, <a href="moose_classes.html#PostMaster.setBufferSize">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.setBufferTime">setBufferTime() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.setBufferTime">[1]</a>, <a href="moose_classes.html#IntFire.setBufferTime">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.setBufferTime">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.setBufferTime">[1]</a>, <a href="moose_classes.html#SynChanBase.setBufferTime">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IzhikevichNrn.setC">setC() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setC">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setC">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#RC.setC">(RC method)</a>, <a href="moose_builtins.html#RC.setC">[1]</a>, <a href="moose_classes.html#RC.setC">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CaConc.setCa">setCa() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setCa">[1]</a>, <a href="moose_classes.html#CaConc.setCa">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.setCa">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setCa">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setCa">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CaConc.setCa_base">setCa_base() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setCa_base">[1]</a>, <a href="moose_classes.html#CaConc.setCa_base">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.setCa_base">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setCa_base">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setCa_base">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HSolve.setCaAdvance">setCaAdvance() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setCaAdvance">[1]</a>, <a href="moose_classes.html#HSolve.setCaAdvance">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.setCaBasal">setCaBasal() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setCaBasal">[1]</a>, <a href="moose_classes.html#CaConc.setCaBasal">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.setCaBasal">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setCaBasal">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setCaBasal">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HSolve.setCaDiv">setCaDiv() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setCaDiv">[1]</a>, <a href="moose_classes.html#HSolve.setCaDiv">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.setCaMax">setCaMax() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setCaMax">[1]</a>, <a href="moose_classes.html#HSolve.setCaMax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.setCaMin">setCaMin() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setCaMin">[1]</a>, <a href="moose_classes.html#HSolve.setCaMin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.setCeiling">setCeiling() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setCeiling">[1]</a>, <a href="moose_classes.html#CaConc.setCeiling">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.setCeiling">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setCeiling">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setCeiling">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.setCell">setCell() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setCell">[1]</a>, <a href="moose_classes.html#NeuroMesh.setCell">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#setCeq">setCeq()</a>, <a href="moose_builtins.html#setCeq">[1]</a>, <a href="moose_classes.html#setCeq">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.setCin">setCin() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.setCin">[1]</a>, <a href="moose_classes.html#Nernst.setCin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Shell.setclock">setclock() (Shell method)</a>, <a href="moose_builtins.html#Shell.setclock">[1]</a>, <a href="moose_classes.html#Shell.setclock">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.setCm">setCm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setCm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setCm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.setCMg">setCMg() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setCMg">[1]</a>, <a href="moose_classes.html#MgBlock.setCMg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.setColor">setColor() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setColor">[1]</a>, <a href="moose_classes.html#Annotator.setColor">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.setCommand">setCommand() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.setCommand">[1]</a>, <a href="moose_classes.html#PIDController.setCommand">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.setCompartment">setCompartment() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setCompartment">[1]</a>, <a href="moose_classes.html#Dsolve.setCompartment">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Ksolve.setCompartment">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setCompartment">[1]</a>, <a href="moose_classes.html#Ksolve.setCompartment">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.setCompartment">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.setCompartment">[1]</a>, <a href="moose_classes.html#Stoich.setCompartment">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PoolBase.setConc">setConc() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setConc">[1]</a>, <a href="moose_classes.html#PoolBase.setConc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.setConcInit">setConcInit() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setConcInit">[1]</a>, <a href="moose_classes.html#PoolBase.setConcInit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.setConcK1">setConcK1() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setConcK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setConcK1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.setconst">setconst() (MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.setconst">[1]</a>, <a href="moose_classes.html#MarkovRateTable.setconst">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.setConvergenceCriterion">setConvergenceCriterion() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setConvergenceCriterion">[1]</a>, <a href="moose_classes.html#SteadyState.setConvergenceCriterion">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.setCoords">setCoords() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setCoords">[1]</a>, <a href="moose_classes.html#CubeMesh.setCoords">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.setCoords">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setCoords">[1]</a>, <a href="moose_classes.html#CylMesh.setCoords">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.setCount">setCount() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setCount">[1]</a>, <a href="moose_classes.html#PulseGen.setCount">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.setCout">setCout() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.setCout">[1]</a>, <a href="moose_classes.html#Nernst.setCout">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#setD">setD()</a>, <a href="moose_builtins.html#setD">[1]</a>, <a href="moose_classes.html#setD">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.setD">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setD">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setD">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.setDelay">setDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setDelay">[1]</a>, <a href="moose_classes.html#PulseGen.setDelay">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Synapse.setDelay">(Synapse method)</a>, <a href="moose_builtins.html#Synapse.setDelay">[1]</a>, <a href="moose_classes.html#Synapse.setDelay">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#setDiameter">setDiameter()</a>, <a href="moose_builtins.html#setDiameter">[1]</a>, <a href="moose_classes.html#setDiameter">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.setDiameter">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setDiameter">[1]</a>, <a href="moose_classes.html#CompartmentBase.setDiameter">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PoolBase.setDiffConst">setDiffConst() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setDiffConst">[1]</a>, <a href="moose_classes.html#PoolBase.setDiffConst">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.setDiffLength">setDiffLength() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setDiffLength">[1]</a>, <a href="moose_classes.html#CylMesh.setDiffLength">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#NeuroMesh.setDiffLength">(NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setDiffLength">[1]</a>, <a href="moose_classes.html#NeuroMesh.setDiffLength">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.setDivs">setDivs() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setDivs">[1]</a>, <a href="moose_classes.html#HHGate.setDivs">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.setDoLoop">setDoLoop() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setDoLoop">[1]</a>, <a href="moose_classes.html#StimulusTable.setDoLoop">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.setDsolve">setDsolve() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setDsolve">[1]</a>, <a href="moose_classes.html#Ksolve.setDsolve">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Stoich.setDsolve">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.setDsolve">[1]</a>, <a href="moose_classes.html#Stoich.setDsolve">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.setDt">setDt() (Clock method)</a>, <a href="moose_builtins.html#Clock.setDt">[1]</a>, <a href="moose_classes.html#Clock.setDt">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HSolve.setDt">(HSolve method)</a>, <a href="moose_builtins.html#HSolve.setDt">[1]</a>, <a href="moose_classes.html#HSolve.setDt">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.setDx">setDx() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setDx">[1]</a>, <a href="moose_classes.html#CubeMesh.setDx">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.setDx">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setDx">[1]</a>, <a href="moose_classes.html#Interpol2D.setDx">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.setDy">setDy() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setDy">[1]</a>, <a href="moose_classes.html#CubeMesh.setDy">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.setDy">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setDy">[1]</a>, <a href="moose_classes.html#Interpol2D.setDy">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.setDz">setDz() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setDz">[1]</a>, <a href="moose_classes.html#CubeMesh.setDz">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.setEdgeTriggered">setEdgeTriggered() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.setEdgeTriggered">[1]</a>, <a href="moose_classes.html#SpikeGen.setEdgeTriggered">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.setEk">setEk() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.setEk">[1]</a>, <a href="moose_classes.html#ChanBase.setEk">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SynChanBase.setEk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.setEk">[1]</a>, <a href="moose_classes.html#SynChanBase.setEk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setEk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setEk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setEk">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.setEm">setEm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setEm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setEm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.setEntry">setEntry() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.setEntry">[1]</a>, <a href="moose_classes.html#SparseMsg.setEntry">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.setEpsAbs">setEpsAbs() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setEpsAbs">[1]</a>, <a href="moose_classes.html#Ksolve.setEpsAbs">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.setEpsRel">setEpsRel() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setEpsRel">[1]</a>, <a href="moose_classes.html#Ksolve.setEpsRel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.setExpr">setExpr() (Func method)</a>, <a href="moose_builtins.html#Func.setExpr">[1]</a>, <a href="moose_classes.html#Func.setExpr">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.setFilename">setFilename() (TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.setFilename">[1]</a>, <a href="moose_classes.html#TimeTable.setFilename">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.setFirstDelay">setFirstDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setFirstDelay">[1]</a>, <a href="moose_classes.html#PulseGen.setFirstDelay">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.setFirstLevel">setFirstLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setFirstLevel">[1]</a>, <a href="moose_classes.html#PulseGen.setFirstLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.setFirstWidth">setFirstWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setFirstWidth">[1]</a>, <a href="moose_classes.html#PulseGen.setFirstWidth">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.setFloor">setFloor() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setFloor">[1]</a>, <a href="moose_classes.html#CaConc.setFloor">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.setFloor">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setFloor">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setFloor">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Arith.setFunction">setFunction() (Arith method)</a>, <a href="moose_builtins.html#Arith.setFunction">[1]</a>, <a href="moose_classes.html#Arith.setFunction">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MathFunc.setFunction">(MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.setFunction">[1]</a>, <a href="moose_classes.html#MathFunc.setFunction">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#DiffAmp.setGain">setGain() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.setGain">[1]</a>, <a href="moose_classes.html#DiffAmp.setGain">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#PIDController.setGain">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.setGain">[1]</a>, <a href="moose_classes.html#PIDController.setGain">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.setGain">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.setGain">[1]</a>, <a href="moose_classes.html#VClamp.setGain">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IzhikevichNrn.setGamma">setGamma() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setGamma">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setGamma">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChanBase.setGbar">setGbar() (ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.setGbar">[1]</a>, <a href="moose_classes.html#ChanBase.setGbar">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovChannel.setGbar">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setGbar">[1]</a>, <a href="moose_classes.html#MarkovChannel.setGbar">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.setGbar">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.setGbar">[1]</a>, <a href="moose_classes.html#SynChanBase.setGbar">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setGbar">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setGbar">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setGbar">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.setGeometryPolicy">setGeometryPolicy() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setGeometryPolicy">[1]</a>, <a href="moose_classes.html#NeuroMesh.setGeometryPolicy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#setGk">setGk()</a>, <a href="moose_builtins.html#setGk">[1]</a>, <a href="moose_classes.html#setGk">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ChanBase.setGk">(ChanBase method)</a>, <a href="moose_builtins.html#ChanBase.setGk">[1]</a>, <a href="moose_classes.html#ChanBase.setGk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.setGk">(SynChanBase method)</a>, <a href="moose_builtins.html#SynChanBase.setGk">[1]</a>, <a href="moose_classes.html#SynChanBase.setGk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setGk">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setGk">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setGk">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#OneToAllMsg.setI1">setI1() (OneToAllMsg method)</a>, <a href="moose_builtins.html#OneToAllMsg.setI1">[1]</a>, <a href="moose_classes.html#OneToAllMsg.setI1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SingleMsg.setI1">(SingleMsg method)</a>, <a href="moose_builtins.html#SingleMsg.setI1">[1]</a>, <a href="moose_classes.html#SingleMsg.setI1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SingleMsg.setI2">setI2() (SingleMsg method)</a>, <a href="moose_builtins.html#SingleMsg.setI2">[1]</a>, <a href="moose_classes.html#SingleMsg.setI2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.setIcon">setIcon() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setIcon">[1]</a>, <a href="moose_classes.html#Annotator.setIcon">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.setIk">setIk() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setIk">[1]</a>, <a href="moose_classes.html#MgBlock.setIk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.setInitialState">setInitialState() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setInitialState">[1]</a>, <a href="moose_classes.html#MarkovChannel.setInitialState">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.setInitialState">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setInitialState">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setInitialState">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IzhikevichNrn.setInitU">setInitU() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setInitU">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setInitU">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.setInitVm">setInitVm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setInitVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setInitVm">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.setInitVm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setInitVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setInitVm">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.setInject">setInject() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setInject">[1]</a>, <a href="moose_classes.html#CompartmentBase.setInject">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.setInject">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setInject">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setInject">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.setInject">(RC method)</a>, <a href="moose_builtins.html#RC.setInject">[1]</a>, <a href="moose_classes.html#RC.setInject">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#setInnerArea">setInnerArea()</a>, <a href="moose_builtins.html#setInnerArea">[1]</a>, <a href="moose_classes.html#setInnerArea">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.setInputOffset">setInputOffset() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.setInputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.setInputOffset">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.setInstant">setInstant() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setInstant">[1]</a>, <a href="moose_classes.html#HHChannel.setInstant">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.setInstant">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setInstant">[1]</a>, <a href="moose_classes.html#HHChannel2D.setInstant">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setInstant">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setInstant">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setInstant">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovGslSolver.setInternalDt">setInternalDt() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.setInternalDt">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.setInternalDt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.setIsToroid">setIsToroid() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setIsToroid">[1]</a>, <a href="moose_classes.html#CubeMesh.setIsToroid">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.setK1">setK1() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setK1">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setK1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.setK2">setK2() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setK2">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setK2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.setK3">setK3() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setK3">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setK3">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.setKb">setKb() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.setKb">[1]</a>, <a href="moose_classes.html#ReacBase.setKb">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.setKcat">setKcat() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.setKcat">[1]</a>, <a href="moose_classes.html#EnzBase.setKcat">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.setKf">setKf() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.setKf">[1]</a>, <a href="moose_classes.html#ReacBase.setKf">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.setKm">setKm() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.setKm">[1]</a>, <a href="moose_classes.html#EnzBase.setKm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.setKMg_A">setKMg_A() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setKMg_A">[1]</a>, <a href="moose_classes.html#MgBlock.setKMg_A">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.setKMg_B">setKMg_B() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setKMg_B">[1]</a>, <a href="moose_classes.html#MgBlock.setKMg_B">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.setKsolve">setKsolve() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.setKsolve">[1]</a>, <a href="moose_classes.html#Stoich.setKsolve">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.setLabels">setLabels() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setLabels">[1]</a>, <a href="moose_classes.html#MarkovChannel.setLabels">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#setLeak">setLeak()</a>, <a href="moose_builtins.html#setLeak">[1]</a>, <a href="moose_classes.html#setLeak">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#setLength">setLength()</a>, <a href="moose_builtins.html#setLength">[1]</a>, <a href="moose_classes.html#setLength">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.setLength">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setLength">[1]</a>, <a href="moose_classes.html#CompartmentBase.setLength">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.setLevel">setLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setLevel">[1]</a>, <a href="moose_classes.html#PulseGen.setLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.setLigandConc">setLigandConc() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setLigandConc">[1]</a>, <a href="moose_classes.html#MarkovChannel.setLigandConc">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovRateTable.setLigandConc">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.setLigandConc">[1]</a>, <a href="moose_classes.html#MarkovRateTable.setLigandConc">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#StimulusTable.setLoopTime">setLoopTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setLoopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.setLoopTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MathFunc.setMathML">setMathML() (MathFunc method)</a>, <a href="moose_builtins.html#MathFunc.setMathML">[1]</a>, <a href="moose_classes.html#MathFunc.setMathML">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.setMax">setMax() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setMax">[1]</a>, <a href="moose_classes.html#HHGate.setMax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.setMaxIter">setMaxIter() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setMaxIter">[1]</a>, <a href="moose_classes.html#SteadyState.setMaxIter">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.setMeshToSpace">setMeshToSpace() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setMeshToSpace">[1]</a>, <a href="moose_classes.html#CubeMesh.setMeshToSpace">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.setMethod">setMethod() (Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setMethod">[1]</a>, <a href="moose_classes.html#Ksolve.setMethod">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovGslSolver.setMethod">(MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.setMethod">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.setMethod">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable.setMethod">(TimeTable method)</a>, <a href="moose_builtins.html#TimeTable.setMethod">[1]</a>, <a href="moose_classes.html#TimeTable.setMethod">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.setMin">setMin() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setMin">[1]</a>, <a href="moose_classes.html#HHGate.setMin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.setMInfinity">setMInfinity() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setMInfinity">[1]</a>, <a href="moose_classes.html#HHGate.setMInfinity">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.setMode">setMode() (Func method)</a>, <a href="moose_builtins.html#Func.setMode">[1]</a>, <a href="moose_classes.html#Func.setMode">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VClamp.setMode">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.setMode">[1]</a>, <a href="moose_classes.html#VClamp.setMode">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Species.setMolWt">setMolWt() (Species method)</a>, <a href="moose_builtins.html#Species.setMolWt">[1]</a>, <a href="moose_classes.html#Species.setMolWt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.setMotorConst">setMotorConst() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setMotorConst">[1]</a>, <a href="moose_classes.html#PoolBase.setMotorConst">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.setN">setN() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setN">[1]</a>, <a href="moose_classes.html#PoolBase.setN">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.setName">setName() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.setName">[1]</a>, <a href="moose_classes.html#Neutral.setName">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.setNInit">setNInit() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setNInit">[1]</a>, <a href="moose_classes.html#PoolBase.setNInit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.setNormalizeWeights">setNormalizeWeights() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.setNormalizeWeights">[1]</a>, <a href="moose_classes.html#SynChan.setNormalizeWeights">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.setNotes">setNotes() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setNotes">[1]</a>, <a href="moose_classes.html#Annotator.setNotes">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve.setNumAllVoxels">setNumAllVoxels() (Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setNumAllVoxels">[1]</a>, <a href="moose_classes.html#Gsolve.setNumAllVoxels">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Ksolve.setNumAllVoxels">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setNumAllVoxels">[1]</a>, <a href="moose_classes.html#Ksolve.setNumAllVoxels">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Neutral.setNumData">setNumData() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.setNumData">[1]</a>, <a href="moose_classes.html#Neutral.setNumData">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.setNumField">setNumField() (Neutral method)</a>, <a href="moose_builtins.html#Neutral.setNumField">[1]</a>, <a href="moose_classes.html#Neutral.setNumField">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.setNumGateX">setNumGateX() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setNumGateX">[1]</a>, <a href="moose_classes.html#HHChannel.setNumGateX">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.setNumGateX">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setNumGateX">[1]</a>, <a href="moose_classes.html#HHChannel2D.setNumGateX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setNumGateX">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setNumGateX">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setNumGateX">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel.setNumGateY">setNumGateY() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setNumGateY">[1]</a>, <a href="moose_classes.html#HHChannel.setNumGateY">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.setNumGateY">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setNumGateY">[1]</a>, <a href="moose_classes.html#HHChannel2D.setNumGateY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setNumGateY">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setNumGateY">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setNumGateY">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel.setNumGateZ">setNumGateZ() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setNumGateZ">[1]</a>, <a href="moose_classes.html#HHChannel.setNumGateZ">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.setNumGateZ">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setNumGateZ">[1]</a>, <a href="moose_classes.html#HHChannel2D.setNumGateZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setNumGateZ">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setNumGateZ">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setNumGateZ">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ReacBase.setNumKb">setNumKb() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.setNumKb">[1]</a>, <a href="moose_classes.html#ReacBase.setNumKb">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ReacBase.setNumKf">setNumKf() (ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.setNumKf">[1]</a>, <a href="moose_classes.html#ReacBase.setNumKf">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.setNumKm">setNumKm() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.setNumKm">[1]</a>, <a href="moose_classes.html#EnzBase.setNumKm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChemCompt.setNumMesh">setNumMesh() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.setNumMesh">[1]</a>, <a href="moose_classes.html#ChemCompt.setNumMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.setNumOpenStates">setNumOpenStates() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setNumOpenStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.setNumOpenStates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.setNumPools">setNumPools() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setNumPools">[1]</a>, <a href="moose_classes.html#Dsolve.setNumPools">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.setNumPools">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setNumPools">[1]</a>, <a href="moose_classes.html#Gsolve.setNumPools">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.setNumPools">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setNumPools">[1]</a>, <a href="moose_classes.html#Ksolve.setNumPools">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovChannel.setNumStates">setNumStates() (MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setNumStates">[1]</a>, <a href="moose_classes.html#MarkovChannel.setNumStates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynHandler.setNumSynapse">setNumSynapse() (SynHandler method)</a>, <a href="moose_builtins.html#SynHandler.setNumSynapse">[1]</a>, <a href="moose_classes.html#SynHandler.setNumSynapse">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynHandler.setNumSynapses">setNumSynapses() (SynHandler method)</a>, <a href="moose_builtins.html#SynHandler.setNumSynapses">[1]</a>, <a href="moose_classes.html#SynHandler.setNumSynapses">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.setNVec">setNVec() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setNVec">[1]</a>, <a href="moose_classes.html#Dsolve.setNVec">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.setNVec">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setNVec">[1]</a>, <a href="moose_classes.html#Gsolve.setNVec">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.setNVec">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setNVec">[1]</a>, <a href="moose_classes.html#Ksolve.setNVec">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.setNx">setNx() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setNx">[1]</a>, <a href="moose_classes.html#CubeMesh.setNx">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.setNy">setNy() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setNy">[1]</a>, <a href="moose_classes.html#CubeMesh.setNy">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.setNz">setNz() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setNz">[1]</a>, <a href="moose_classes.html#CubeMesh.setNz">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#setOuterArea">setOuterArea()</a>, <a href="moose_builtins.html#setOuterArea">[1]</a>, <a href="moose_classes.html#setOuterArea">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Adaptor.setOutputOffset">setOutputOffset() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.setOutputOffset">[1]</a>, <a href="moose_classes.html#Adaptor.setOutputOffset">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Arith.setOutputValue">setOutputValue() (Arith method)</a>, <a href="moose_builtins.html#Arith.setOutputValue">[1]</a>, <a href="moose_classes.html#Arith.setOutputValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.setPath">setPath() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setPath">[1]</a>, <a href="moose_classes.html#Dsolve.setPath">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Stoich.setPath">(Stoich method)</a>, <a href="moose_builtins.html#Stoich.setPath">[1]</a>, <a href="moose_classes.html#Stoich.setPath">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.setPreserveNumEntries">setPreserveNumEntries() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setPreserveNumEntries">[1]</a>, <a href="moose_classes.html#CubeMesh.setPreserveNumEntries">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.setProbability">setProbability() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.setProbability">[1]</a>, <a href="moose_classes.html#SparseMsg.setProbability">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.setR">setR() (RC method)</a>, <a href="moose_builtins.html#RC.setR">[1]</a>, <a href="moose_classes.html#RC.setR">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.setR0">setR0() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setR0">[1]</a>, <a href="moose_classes.html#CylMesh.setR0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.setR1">setR1() (CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setR1">[1]</a>, <a href="moose_classes.html#CylMesh.setR1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.setRa">setRa() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setRa">[1]</a>, <a href="moose_classes.html#CompartmentBase.setRa">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.setRandomConnectivity">setRandomConnectivity() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.setRandomConnectivity">[1]</a>, <a href="moose_classes.html#SparseMsg.setRandomConnectivity">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CplxEnzBase.setRatio">setRatio() (CplxEnzBase method)</a>, <a href="moose_builtins.html#CplxEnzBase.setRatio">[1]</a>, <a href="moose_classes.html#CplxEnzBase.setRatio">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.setRefractoryPeriod">setRefractoryPeriod() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.setRefractoryPeriod">[1]</a>, <a href="moose_classes.html#IntFire.setRefractoryPeriod">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.setRefractT">setRefractT() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.setRefractT">[1]</a>, <a href="moose_classes.html#SpikeGen.setRefractT">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovGslSolver.setRelativeAccuracy">setRelativeAccuracy() (MarkovGslSolver method)</a>, <a href="moose_builtins.html#MarkovGslSolver.setRelativeAccuracy">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.setRelativeAccuracy">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#CompartmentBase.setRm">setRm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setRm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setRm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.setRmByTau">setRmByTau() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setRmByTau">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setRmByTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiffAmp.setSaturation">setSaturation() (DiffAmp method)</a>, <a href="moose_builtins.html#DiffAmp.setSaturation">[1]</a>, <a href="moose_classes.html#DiffAmp.setSaturation">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#PIDController.setSaturation">(PIDController method)</a>, <a href="moose_builtins.html#PIDController.setSaturation">[1]</a>, <a href="moose_classes.html#PIDController.setSaturation">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Adaptor.setScale">setScale() (Adaptor method)</a>, <a href="moose_builtins.html#Adaptor.setScale">[1]</a>, <a href="moose_classes.html#Adaptor.setScale">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Nernst.setScale">(Nernst method)</a>, <a href="moose_builtins.html#Nernst.setScale">[1]</a>, <a href="moose_classes.html#Nernst.setScale">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#PulseGen.setSecondDelay">setSecondDelay() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setSecondDelay">[1]</a>, <a href="moose_classes.html#PulseGen.setSecondDelay">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.setSecondLevel">setSecondLevel() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setSecondLevel">[1]</a>, <a href="moose_classes.html#PulseGen.setSecondLevel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.setSecondWidth">setSecondWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setSecondWidth">[1]</a>, <a href="moose_classes.html#PulseGen.setSecondWidth">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.setSeed">setSeed() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setSeed">[1]</a>, <a href="moose_classes.html#HSolve.setSeed">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SparseMsg.setSeed">(SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.setSeed">[1]</a>, <a href="moose_classes.html#SparseMsg.setSeed">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.setSeparateSpines">setSeparateSpines() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setSeparateSpines">[1]</a>, <a href="moose_classes.html#NeuroMesh.setSeparateSpines">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#setShapeMode">setShapeMode()</a>, <a href="moose_builtins.html#setShapeMode">[1]</a>, <a href="moose_classes.html#setShapeMode">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.setSpaceToMesh">setSpaceToMesh() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setSpaceToMesh">[1]</a>, <a href="moose_classes.html#CubeMesh.setSpaceToMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.setSpeciesId">setSpeciesId() (PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setSpeciesId">[1]</a>, <a href="moose_classes.html#PoolBase.setSpeciesId">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.setStartTime">setStartTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setStartTime">[1]</a>, <a href="moose_classes.html#StimulusTable.setStartTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.setStepPosition">setStepPosition() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setStepPosition">[1]</a>, <a href="moose_classes.html#StimulusTable.setStepPosition">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.setStepSize">setStepSize() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setStepSize">[1]</a>, <a href="moose_classes.html#StimulusTable.setStepSize">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.setStoich">setStoich() (Dsolve method)</a>, <a href="moose_builtins.html#Dsolve.setStoich">[1]</a>, <a href="moose_classes.html#Dsolve.setStoich">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.setStoich">(Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setStoich">[1]</a>, <a href="moose_classes.html#Gsolve.setStoich">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.setStoich">(Ksolve method)</a>, <a href="moose_builtins.html#Ksolve.setStoich">[1]</a>, <a href="moose_classes.html#Ksolve.setStoich">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.setStoich">(SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setStoich">[1]</a>, <a href="moose_classes.html#SteadyState.setStoich">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#StimulusTable.setStopTime">setStopTime() (StimulusTable method)</a>, <a href="moose_builtins.html#StimulusTable.setStopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.setStopTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiagonalMsg.setStride">setStride() (DiagonalMsg method)</a>, <a href="moose_builtins.html#DiagonalMsg.setStride">[1]</a>, <a href="moose_classes.html#DiagonalMsg.setStride">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh.setSubTree">setSubTree() (NeuroMesh method)</a>, <a href="moose_builtins.html#NeuroMesh.setSubTree">[1]</a>, <a href="moose_classes.html#NeuroMesh.setSubTree">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.setSurface">setSurface() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setSurface">[1]</a>, <a href="moose_classes.html#CubeMesh.setSurface">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.setTable">setTable() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setTable">[1]</a>, <a href="moose_classes.html#Interpol2D.setTable">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VectorTable.setTable">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.setTable">[1]</a>, <a href="moose_classes.html#VectorTable.setTable">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.setTableA">setTableA() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setTableA">[1]</a>, <a href="moose_classes.html#HHGate.setTableA">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate2D.setTableA">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setTableA">[1]</a>, <a href="moose_classes.html#HHGate2D.setTableA">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.setTableB">setTableB() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setTableB">[1]</a>, <a href="moose_classes.html#HHGate.setTableB">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate2D.setTableB">(HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setTableB">[1]</a>, <a href="moose_classes.html#HHGate2D.setTableB">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.setTableVector2D">setTableVector2D() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setTableVector2D">[1]</a>, <a href="moose_classes.html#Interpol2D.setTableVector2D">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.setTarget">setTarget() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setTarget">[1]</a>, <a href="moose_classes.html#HSolve.setTarget">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.setTau">setTau() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setTau">[1]</a>, <a href="moose_classes.html#CaConc.setTau">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate.setTau">(HHGate method)</a>, <a href="moose_builtins.html#HHGate.setTau">[1]</a>, <a href="moose_classes.html#HHGate.setTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.setTau">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.setTau">[1]</a>, <a href="moose_classes.html#IntFire.setTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.setTau">(VClamp method)</a>, <a href="moose_builtins.html#VClamp.setTau">[1]</a>, <a href="moose_classes.html#VClamp.setTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCaConc.setTau">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setTau">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setTau">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SynChan.setTau1">setTau1() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.setTau1">[1]</a>, <a href="moose_classes.html#SynChan.setTau1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.setTau2">setTau2() (SynChan method)</a>, <a href="moose_builtins.html#SynChan.setTau2">[1]</a>, <a href="moose_classes.html#SynChan.setTau2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.setTauD">setTauD() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.setTauD">[1]</a>, <a href="moose_classes.html#PIDController.setTauD">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.setTauI">setTauI() (PIDController method)</a>, <a href="moose_builtins.html#PIDController.setTauI">[1]</a>, <a href="moose_classes.html#PIDController.setTauI">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp.setTd">setTd() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.setTd">[1]</a>, <a href="moose_classes.html#VClamp.setTd">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.setTemperature">setTemperature() (Nernst method)</a>, <a href="moose_builtins.html#Nernst.setTemperature">[1]</a>, <a href="moose_classes.html#Nernst.setTemperature">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.setTextColor">setTextColor() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setTextColor">[1]</a>, <a href="moose_classes.html#Annotator.setTextColor">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CaConc.setThick">setThick() (CaConc method)</a>, <a href="moose_builtins.html#CaConc.setThick">[1]</a>, <a href="moose_classes.html#CaConc.setThick">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.setThick">(ZombieCaConc method)</a>, <a href="moose_builtins.html#ZombieCaConc.setThick">[1]</a>, <a href="moose_classes.html#ZombieCaConc.setThick">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#setThickness">setThickness()</a>, <a href="moose_builtins.html#setThickness">[1]</a>, <a href="moose_classes.html#setThickness">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#PsdMesh.setThickness">(PsdMesh method)</a>, <a href="moose_builtins.html#PsdMesh.setThickness">[1]</a>, <a href="moose_classes.html#PsdMesh.setThickness">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Mstring.setThis">setThis() (Mstring method)</a>, <a href="moose_builtins.html#Mstring.setThis">[1]</a>, <a href="moose_classes.html#Mstring.setThis">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Neutral.setThis">(Neutral method)</a>, <a href="moose_builtins.html#Neutral.setThis">[1]</a>, <a href="moose_classes.html#Neutral.setThis">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IntFire.setThresh">setThresh() (IntFire method)</a>, <a href="moose_builtins.html#IntFire.setThresh">[1]</a>, <a href="moose_classes.html#IntFire.setThresh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.setThreshold">setThreshold() (SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.setThreshold">[1]</a>, <a href="moose_classes.html#SpikeGen.setThreshold">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Table.setThreshold">(Table method)</a>, <a href="moose_builtins.html#Table.setThreshold">[1]</a>, <a href="moose_classes.html#Table.setThreshold">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#VClamp.setTi">setTi() (VClamp method)</a>, <a href="moose_builtins.html#VClamp.setTi">[1]</a>, <a href="moose_classes.html#VClamp.setTi">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.setTickDt">setTickDt() (Clock method)</a>, <a href="moose_builtins.html#Clock.setTickDt">[1]</a>, <a href="moose_classes.html#Clock.setTickDt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.setTickStep">setTickStep() (Clock method)</a>, <a href="moose_builtins.html#Clock.setTickStep">[1]</a>, <a href="moose_classes.html#Clock.setTickStep">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.settle">settle() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.settle">[1]</a>, <a href="moose_classes.html#SteadyState.settle">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.setTotal">setTotal() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setTotal">[1]</a>, <a href="moose_classes.html#SteadyState.setTotal">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.setTrigMode">setTrigMode() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setTrigMode">[1]</a>, <a href="moose_classes.html#PulseGen.setTrigMode">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.setU0">setU0() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setU0">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setU0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.setupAlpha">setupAlpha() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setupAlpha">[1]</a>, <a href="moose_classes.html#HHGate.setupAlpha">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.setupGate">setupGate() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setupGate">[1]</a>, <a href="moose_classes.html#HHGate.setupGate">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.setupMatrix">setupMatrix() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.setupMatrix">[1]</a>, <a href="moose_classes.html#SteadyState.setupMatrix">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.setupTau">setupTau() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setupTau">[1]</a>, <a href="moose_classes.html#HHGate.setupTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.setUseConcentration">setUseConcentration() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setUseConcentration">[1]</a>, <a href="moose_classes.html#HHChannel.setUseConcentration">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieHHChannel.setUseConcentration">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setUseConcentration">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setUseConcentration">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.setUseInterpolation">setUseInterpolation() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.setUseInterpolation">[1]</a>, <a href="moose_classes.html#HHGate.setUseInterpolation">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve.setUseRandInit">setUseRandInit() (Gsolve method)</a>, <a href="moose_builtins.html#Gsolve.setUseRandInit">[1]</a>, <a href="moose_classes.html#Gsolve.setUseRandInit">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.setV0">setV0() (RC method)</a>, <a href="moose_builtins.html#RC.setV0">[1]</a>, <a href="moose_classes.html#RC.setV0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#setValence">setValence()</a>, <a href="moose_builtins.html#setValence">[1]</a>, <a href="moose_classes.html#setValence">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Nernst.setValence">(Nernst method)</a>, <a href="moose_builtins.html#Nernst.setValence">[1]</a>, <a href="moose_classes.html#Nernst.setValence">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Double.setValue">setValue() (Double method)</a>, <a href="moose_builtins.html#Double.setValue">[1]</a>, <a href="moose_classes.html#Double.setValue">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Long.setValue">(Long method)</a>, <a href="moose_builtins.html#Long.setValue">[1]</a>, <a href="moose_classes.html#Long.setValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Mstring.setValue">(Mstring method)</a>, <a href="moose_builtins.html#Mstring.setValue">[1]</a>, <a href="moose_classes.html#Mstring.setValue">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Unsigned.setValue">(Unsigned method)</a>, <a href="moose_builtins.html#Unsigned.setValue">[1]</a>, <a href="moose_classes.html#Unsigned.setValue">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Func.setVar">setVar() (Func method)</a>, <a href="moose_builtins.html#Func.setVar">[1]</a>, <a href="moose_classes.html#Func.setVar">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.setVDiv">setVDiv() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setVDiv">[1]</a>, <a href="moose_classes.html#HSolve.setVDiv">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.setVector">setVector() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.setVector">[1]</a>, <a href="moose_classes.html#TableBase.setVector">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.setVm">setVm() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setVm">[1]</a>, <a href="moose_classes.html#CompartmentBase.setVm">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IntFire.setVm">(IntFire method)</a>, <a href="moose_builtins.html#IntFire.setVm">[1]</a>, <a href="moose_classes.html#IntFire.setVm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.setVm">(IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setVm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setVm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.setVm">(MarkovChannel method)</a>, <a href="moose_builtins.html#MarkovChannel.setVm">[1]</a>, <a href="moose_classes.html#MarkovChannel.setVm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.setVm">(MarkovRateTable method)</a>, <a href="moose_builtins.html#MarkovRateTable.setVm">[1]</a>, <a href="moose_classes.html#MarkovRateTable.setVm">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HSolve.setVMax">setVMax() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setVMax">[1]</a>, <a href="moose_classes.html#HSolve.setVMax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.setVmax">setVmax() (IzhikevichNrn method)</a>, <a href="moose_builtins.html#IzhikevichNrn.setVmax">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.setVmax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.setVMin">setVMin() (HSolve method)</a>, <a href="moose_builtins.html#HSolve.setVMin">[1]</a>, <a href="moose_classes.html#HSolve.setVMin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#setVolume">setVolume()</a>, <a href="moose_builtins.html#setVolume">[1]</a>, <a href="moose_classes.html#setVolume">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ChemCompt.setVolume">(ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.setVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.setVolume">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.setVolume">(PoolBase method)</a>, <a href="moose_builtins.html#PoolBase.setVolume">[1]</a>, <a href="moose_classes.html#PoolBase.setVolume">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChemCompt.setVolumeNotRates">setVolumeNotRates() (ChemCompt method)</a>, <a href="moose_builtins.html#ChemCompt.setVolumeNotRates">[1]</a>, <a href="moose_classes.html#ChemCompt.setVolumeNotRates">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Synapse.setWeight">setWeight() (Synapse method)</a>, <a href="moose_builtins.html#Synapse.setWeight">[1]</a>, <a href="moose_classes.html#Synapse.setWeight">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.setWidth">setWidth() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.setWidth">[1]</a>, <a href="moose_classes.html#PulseGen.setWidth">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.setX">setX() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setX">[1]</a>, <a href="moose_classes.html#Annotator.setX">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.setX">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setX">[1]</a>, <a href="moose_classes.html#CompartmentBase.setX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.setX">(Func method)</a>, <a href="moose_builtins.html#Func.setX">[1]</a>, <a href="moose_classes.html#Func.setX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.setX">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setX">[1]</a>, <a href="moose_classes.html#HHChannel.setX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.setX">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setX">[1]</a>, <a href="moose_classes.html#HHChannel2D.setX">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setX">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setX">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setX">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.setX0">setX0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setX0">[1]</a>, <a href="moose_classes.html#CompartmentBase.setX0">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CubeMesh.setX0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setX0">[1]</a>, <a href="moose_classes.html#CubeMesh.setX0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.setX0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setX0">[1]</a>, <a href="moose_classes.html#CylMesh.setX0">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.setX1">setX1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setX1">[1]</a>, <a href="moose_classes.html#CubeMesh.setX1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.setX1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setX1">[1]</a>, <a href="moose_classes.html#CylMesh.setX1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.setXdivs">setXdivs() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setXdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.setXdivs">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.setXdivs">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setXdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setXdivs">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.setXdivs">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.setXdivs">[1]</a>, <a href="moose_classes.html#VectorTable.setXdivs">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.setXdivsA">setXdivsA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.setXdivsA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.setXdivsB">setXdivsB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.setXdivsB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.setXindex">setXindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setXindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.setXindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.setXmax">setXmax() (Interpol method)</a>, <a href="moose_builtins.html#Interpol.setXmax">[1]</a>, <a href="moose_classes.html#Interpol.setXmax">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.setXmax">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setXmax">[1]</a>, <a href="moose_classes.html#Interpol2D.setXmax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.setXmax">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setXmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setXmax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.setXmax">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.setXmax">[1]</a>, <a href="moose_classes.html#VectorTable.setXmax">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.setXmaxA">setXmaxA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.setXmaxA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.setXmaxB">setXmaxB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.setXmaxB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.setXmin">setXmin() (Interpol method)</a>, <a href="moose_builtins.html#Interpol.setXmin">[1]</a>, <a href="moose_classes.html#Interpol.setXmin">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.setXmin">(Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setXmin">[1]</a>, <a href="moose_classes.html#Interpol2D.setXmin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.setXmin">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setXmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setXmin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.setXmin">(VectorTable method)</a>, <a href="moose_builtins.html#VectorTable.setXmin">[1]</a>, <a href="moose_classes.html#VectorTable.setXmin">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.setXminA">setXminA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXminA">[1]</a>, <a href="moose_classes.html#HHGate2D.setXminA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.setXminB">setXminB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setXminB">[1]</a>, <a href="moose_classes.html#HHGate2D.setXminB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.setXpower">setXpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setXpower">[1]</a>, <a href="moose_classes.html#HHChannel.setXpower">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.setXpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setXpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.setXpower">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setXpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setXpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setXpower">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Annotator.setY">setY() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setY">[1]</a>, <a href="moose_classes.html#Annotator.setY">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.setY">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setY">[1]</a>, <a href="moose_classes.html#CompartmentBase.setY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.setY">(Func method)</a>, <a href="moose_builtins.html#Func.setY">[1]</a>, <a href="moose_classes.html#Func.setY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.setY">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setY">[1]</a>, <a href="moose_classes.html#HHChannel.setY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.setY">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setY">[1]</a>, <a href="moose_classes.html#HHChannel2D.setY">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setY">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setY">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setY">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.setY0">setY0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setY0">[1]</a>, <a href="moose_classes.html#CompartmentBase.setY0">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CubeMesh.setY0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setY0">[1]</a>, <a href="moose_classes.html#CubeMesh.setY0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.setY0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setY0">[1]</a>, <a href="moose_classes.html#CylMesh.setY0">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.setY1">setY1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setY1">[1]</a>, <a href="moose_classes.html#CubeMesh.setY1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.setY1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setY1">[1]</a>, <a href="moose_classes.html#CylMesh.setY1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.setYdivs">setYdivs() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setYdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.setYdivs">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.setYdivs">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setYdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setYdivs">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.setYdivsA">setYdivsA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.setYdivsA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.setYdivsB">setYdivsB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.setYdivsB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.setYindex">setYindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setYindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.setYindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.setYmax">setYmax() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setYmax">[1]</a>, <a href="moose_classes.html#Interpol2D.setYmax">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.setYmax">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setYmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setYmax">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.setYmaxA">setYmaxA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.setYmaxA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.setYmaxB">setYmaxB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.setYmaxB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.setYmin">setYmin() (Interpol2D method)</a>, <a href="moose_builtins.html#Interpol2D.setYmin">[1]</a>, <a href="moose_classes.html#Interpol2D.setYmin">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.setYmin">(MarkovSolverBase method)</a>, <a href="moose_builtins.html#MarkovSolverBase.setYmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.setYmin">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.setYminA">setYminA() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYminA">[1]</a>, <a href="moose_classes.html#HHGate2D.setYminA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.setYminB">setYminB() (HHGate2D method)</a>, <a href="moose_builtins.html#HHGate2D.setYminB">[1]</a>, <a href="moose_classes.html#HHGate2D.setYminB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.setYpower">setYpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setYpower">[1]</a>, <a href="moose_classes.html#HHChannel.setYpower">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.setYpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setYpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.setYpower">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setYpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setYpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setYpower">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Annotator.setZ">setZ() (Annotator method)</a>, <a href="moose_builtins.html#Annotator.setZ">[1]</a>, <a href="moose_classes.html#Annotator.setZ">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CompartmentBase.setZ">(CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setZ">[1]</a>, <a href="moose_classes.html#CompartmentBase.setZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.setZ">(Func method)</a>, <a href="moose_builtins.html#Func.setZ">[1]</a>, <a href="moose_classes.html#Func.setZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.setZ">(HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setZ">[1]</a>, <a href="moose_classes.html#HHChannel.setZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.setZ">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setZ">[1]</a>, <a href="moose_classes.html#HHChannel2D.setZ">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setZ">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setZ">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setZ">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.setZ0">setZ0() (CompartmentBase method)</a>, <a href="moose_builtins.html#CompartmentBase.setZ0">[1]</a>, <a href="moose_classes.html#CompartmentBase.setZ0">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CubeMesh.setZ0">(CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setZ0">[1]</a>, <a href="moose_classes.html#CubeMesh.setZ0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.setZ0">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setZ0">[1]</a>, <a href="moose_classes.html#CylMesh.setZ0">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.setZ1">setZ1() (CubeMesh method)</a>, <a href="moose_builtins.html#CubeMesh.setZ1">[1]</a>, <a href="moose_classes.html#CubeMesh.setZ1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.setZ1">(CylMesh method)</a>, <a href="moose_builtins.html#CylMesh.setZ1">[1]</a>, <a href="moose_classes.html#CylMesh.setZ1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel2D.setZindex">setZindex() (HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setZindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.setZindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.setZk">setZk() (MgBlock method)</a>, <a href="moose_builtins.html#MgBlock.setZk">[1]</a>, <a href="moose_classes.html#MgBlock.setZk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.setZpower">setZpower() (HHChannel method)</a>, <a href="moose_builtins.html#HHChannel.setZpower">[1]</a>, <a href="moose_classes.html#HHChannel.setZpower">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.setZpower">(HHChannel2D method)</a>, <a href="moose_builtins.html#HHChannel2D.setZpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.setZpower">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.setZpower">(ZombieHHChannel method)</a>, <a href="moose_builtins.html#ZombieHHChannel.setZpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.setZpower">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#shapeMode">shapeMode</a>, <a href="moose_builtins.html#shapeMode">[1]</a>, <a href="moose_classes.html#shapeMode">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Shell">Shell (built-in class)</a>, <a href="moose_builtins.html#Shell">[1]</a>, <a href="moose_classes.html#Shell">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.showMatrices">showMatrices() (SteadyState method)</a>, <a href="moose_builtins.html#SteadyState.showMatrices">[1]</a>, <a href="moose_classes.html#SteadyState.showMatrices">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#sibling">sibling</a>, <a href="moose_builtins.html#sibling">[1]</a>, <a href="moose_classes.html#sibling">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SingleMsg">SingleMsg (built-in class)</a>, <a href="moose_builtins.html#SingleMsg">[1]</a>, <a href="moose_classes.html#SingleMsg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.size">size (MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.size">[1]</a>, <a href="moose_classes.html#MarkovRateTable.size">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#TableBase.size">(TableBase attribute)</a>, <a href="moose_builtins.html#TableBase.size">[1]</a>, <a href="moose_classes.html#TableBase.size">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SteadyState.solutionStatus">solutionStatus (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.solutionStatus">[1]</a>, <a href="moose_classes.html#SteadyState.solutionStatus">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Neutral.sourceFields">sourceFields (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.sourceFields">[1]</a>, <a href="moose_classes.html#Neutral.sourceFields">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.spaceToMesh">spaceToMesh (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.spaceToMesh">[1]</a>, <a href="moose_classes.html#CubeMesh.spaceToMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg">SparseMsg (built-in class)</a>, <a href="moose_builtins.html#SparseMsg">[1]</a>, <a href="moose_classes.html#SparseMsg">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Species">Species (built-in class)</a>, <a href="moose_builtins.html#Species">[1]</a>, <a href="moose_classes.html#Species">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.species">species (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.species">[1]</a>, <a href="moose_classes.html#PoolBase.species">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.speciesId">speciesId (PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.speciesId">[1]</a>, <a href="moose_classes.html#PoolBase.speciesId">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#sphere">sphere</a>, <a href="moose_builtins.html#sphere">[1]</a>, <a href="moose_classes.html#sphere">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Table.spike">spike() (Table method)</a>, <a href="moose_builtins.html#Table.spike">[1]</a>, <a href="moose_classes.html#Table.spike">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen">SpikeGen (built-in class)</a>, <a href="moose_builtins.html#SpikeGen">[1]</a>, <a href="moose_classes.html#SpikeGen">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.spikeOut">spikeOut (IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.spikeOut">[1]</a>, <a href="moose_classes.html#IntFire.spikeOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.spikeOut">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.spikeOut">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.spikeOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.spikeOut">(SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.spikeOut">[1]</a>, <a href="moose_classes.html#SpikeGen.spikeOut">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SpineMesh.spineList">spineList() (SpineMesh method)</a>, <a href="moose_builtins.html#SpineMesh.spineList">[1]</a>, <a href="moose_classes.html#SpineMesh.spineList">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#NeuroMesh.spineListOut">spineListOut (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.spineListOut">[1]</a>, <a href="moose_classes.html#NeuroMesh.spineListOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpineMesh">SpineMesh (built-in class)</a>, <a href="moose_builtins.html#SpineMesh">[1]</a>, <a href="moose_classes.html#SpineMesh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Finfo.src">src (Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.src">[1]</a>, <a href="moose_classes.html#Finfo.src">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.srcFieldsOnE1">srcFieldsOnE1 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.srcFieldsOnE1">[1]</a>, <a href="moose_classes.html#Msg.srcFieldsOnE1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Msg.srcFieldsOnE2">srcFieldsOnE2 (Msg attribute)</a>, <a href="moose_builtins.html#Msg.srcFieldsOnE2">[1]</a>, <a href="moose_classes.html#Msg.srcFieldsOnE2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.start">start() (Clock method)</a>, <a href="moose_builtins.html#Clock.start">[1]</a>, <a href="moose_classes.html#Clock.start">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.startTime">startTime (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.startTime">[1]</a>, <a href="moose_classes.html#StimulusTable.startTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#state">state</a>, <a href="moose_builtins.html#state">[1]</a>, <a href="moose_classes.html#state">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovChannel.state">(MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.state">[1]</a>, <a href="moose_classes.html#MarkovChannel.state">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.state">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.state">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.state">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#RC.state">(RC attribute)</a>, <a href="moose_builtins.html#RC.state">[1]</a>, <a href="moose_classes.html#RC.state">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#MarkovGslSolver.stateOut">stateOut (MarkovGslSolver attribute)</a>, <a href="moose_builtins.html#MarkovGslSolver.stateOut">[1]</a>, <a href="moose_classes.html#MarkovGslSolver.stateOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.stateOut">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.stateOut">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.stateOut">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SteadyState.stateType">stateType (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.stateType">[1]</a>, <a href="moose_classes.html#SteadyState.stateType">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats">Stats (built-in class)</a>, <a href="moose_builtins.html#Stats">[1]</a>, <a href="moose_classes.html#Stats">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.status">status (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.status">[1]</a>, <a href="moose_classes.html#SteadyState.status">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState">SteadyState (built-in class)</a>, <a href="moose_builtins.html#SteadyState">[1]</a>, <a href="moose_classes.html#SteadyState">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChemCompt.stencilIndex">stencilIndex (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.stencilIndex">[1]</a>, <a href="moose_classes.html#ChemCompt.stencilIndex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ChemCompt.stencilRate">stencilRate (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.stencilRate">[1]</a>, <a href="moose_classes.html#ChemCompt.stencilRate">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.step">step() (Clock method)</a>, <a href="moose_builtins.html#Clock.step">[1]</a>, <a href="moose_classes.html#Clock.step">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.stepPosition">stepPosition (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.stepPosition">[1]</a>, <a href="moose_classes.html#StimulusTable.stepPosition">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.stepSize">stepSize (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.stepSize">[1]</a>, <a href="moose_classes.html#StimulusTable.stepSize">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable">StimulusTable (built-in class)</a>, <a href="moose_builtins.html#StimulusTable">[1]</a>, <a href="moose_classes.html#StimulusTable">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich">Stoich (built-in class)</a>, <a href="moose_builtins.html#Stoich">[1]</a>, <a href="moose_classes.html#Stoich">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Dsolve.stoich">stoich (Dsolve attribute)</a>, <a href="moose_builtins.html#Dsolve.stoich">[1]</a>, <a href="moose_classes.html#Dsolve.stoich">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Gsolve.stoich">(Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.stoich">[1]</a>, <a href="moose_classes.html#Gsolve.stoich">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Ksolve.stoich">(Ksolve attribute)</a>, <a href="moose_builtins.html#Ksolve.stoich">[1]</a>, <a href="moose_classes.html#Ksolve.stoich">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.stoich">(SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.stoich">[1]</a>, <a href="moose_classes.html#SteadyState.stoich">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Clock.stop">stop() (Clock method)</a>, <a href="moose_builtins.html#Clock.stop">[1]</a>, <a href="moose_classes.html#Clock.stop">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#StimulusTable.stopTime">stopTime (StimulusTable attribute)</a>, <a href="moose_builtins.html#StimulusTable.stopTime">[1]</a>, <a href="moose_classes.html#StimulusTable.stopTime">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#storeInflux">storeInflux()</a>, <a href="moose_builtins.html#storeInflux">[1]</a>, <a href="moose_classes.html#storeInflux">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#storeOutflux">storeOutflux()</a>, <a href="moose_builtins.html#storeOutflux">[1]</a>, <a href="moose_classes.html#storeOutflux">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#DiagonalMsg.stride">stride (DiagonalMsg attribute)</a>, <a href="moose_builtins.html#DiagonalMsg.stride">[1]</a>, <a href="moose_classes.html#DiagonalMsg.stride">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#EnzBase.sub">sub (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.sub">[1]</a>, <a href="moose_classes.html#EnzBase.sub">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ReacBase.sub">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.sub">[1]</a>, <a href="moose_classes.html#ReacBase.sub">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#EnzBase.subDest">subDest() (EnzBase method)</a>, <a href="moose_builtins.html#EnzBase.subDest">[1]</a>, <a href="moose_classes.html#EnzBase.subDest">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ReacBase.subDest">(ReacBase method)</a>, <a href="moose_builtins.html#ReacBase.subDest">[1]</a>, <a href="moose_classes.html#ReacBase.subDest">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#EnzBase.subOut">subOut (EnzBase attribute)</a>, <a href="moose_builtins.html#EnzBase.subOut">[1]</a>, <a href="moose_classes.html#EnzBase.subOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ReacBase.subOut">(ReacBase attribute)</a>, <a href="moose_builtins.html#ReacBase.subOut">[1]</a>, <a href="moose_classes.html#ReacBase.subOut">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#NeuroMesh.subTree">subTree (NeuroMesh attribute)</a>, <a href="moose_builtins.html#NeuroMesh.subTree">[1]</a>, <a href="moose_classes.html#NeuroMesh.subTree">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stats.sum">sum (Stats attribute)</a>, <a href="moose_builtins.html#Stats.sum">[1]</a>, <a href="moose_classes.html#Stats.sum">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SumFunc">SumFunc (built-in class)</a>, <a href="moose_builtins.html#SumFunc">[1]</a>, <a href="moose_classes.html#SumFunc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#sumRaxial">sumRaxial()</a>, <a href="tmp.html#sumRaxial">[1]</a>, <a href="tmp.html#sumRaxial">[2]</a>, <a href="moose_builtins.html#sumRaxial">[3]</a>, <a href="moose_builtins.html#sumRaxial">[4]</a>, <a href="moose_builtins.html#sumRaxial">[5]</a>, <a href="moose_classes.html#sumRaxial">[6]</a>, <a href="moose_classes.html#sumRaxial">[7]</a>, <a href="moose_classes.html#sumRaxial">[8]</a>
- </dt>
-
-
- <dt><a href="tmp.html#sumRaxialOut">sumRaxialOut</a>, <a href="tmp.html#sumRaxialOut">[1]</a>, <a href="tmp.html#sumRaxialOut">[2]</a>, <a href="moose_builtins.html#sumRaxialOut">[3]</a>, <a href="moose_builtins.html#sumRaxialOut">[4]</a>, <a href="moose_builtins.html#sumRaxialOut">[5]</a>, <a href="moose_classes.html#sumRaxialOut">[6]</a>, <a href="moose_classes.html#sumRaxialOut">[7]</a>, <a href="moose_classes.html#sumRaxialOut">[8]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CubeMesh.surface">surface (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.surface">[1]</a>, <a href="moose_classes.html#CubeMesh.surface">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SymCompartment">SymCompartment (built-in class)</a>, <a href="moose_builtins.html#SymCompartment">[1]</a>, <a href="moose_classes.html#SymCompartment">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Synapse">Synapse (built-in class)</a>, <a href="moose_builtins.html#Synapse">[1]</a>, <a href="moose_classes.html#Synapse">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan">SynChan (built-in class)</a>, <a href="moose_builtins.html#SynChan">[1]</a>, <a href="moose_classes.html#SynChan">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase">SynChanBase (built-in class)</a>, <a href="moose_builtins.html#SynChanBase">[1]</a>, <a href="moose_classes.html#SynChanBase">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynHandler">SynHandler (built-in class)</a>, <a href="moose_builtins.html#SynHandler">[1]</a>, <a href="moose_classes.html#SynHandler">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="T">T</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Table">Table (built-in class)</a>, <a href="moose_builtins.html#Table">[1]</a>, <a href="moose_classes.html#Table">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.table">table (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.table">[1]</a>, <a href="moose_classes.html#Interpol2D.table">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#VectorTable.table">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.table">[1]</a>, <a href="moose_classes.html#VectorTable.table">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.tableA">tableA (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.tableA">[1]</a>, <a href="moose_classes.html#HHGate.tableA">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate2D.tableA">(HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.tableA">[1]</a>, <a href="moose_classes.html#HHGate2D.tableA">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.tableB">tableB (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.tableB">[1]</a>, <a href="moose_classes.html#HHGate.tableB">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHGate2D.tableB">(HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.tableB">[1]</a>, <a href="moose_classes.html#HHGate2D.tableB">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#TableBase">TableBase (built-in class)</a>, <a href="moose_builtins.html#TableBase">[1]</a>, <a href="moose_classes.html#TableBase">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.tableVector2D">tableVector2D (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.tableVector2D">[1]</a>, <a href="moose_classes.html#Interpol2D.tableVector2D">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.target">target (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.target">[1]</a>, <a href="moose_classes.html#HSolve.target">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#tau">tau</a>, <a href="moose_builtins.html#tau">[1]</a>, <a href="moose_classes.html#tau">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CaConc.tau">(CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.tau">[1]</a>, <a href="moose_classes.html#CaConc.tau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.tau">(HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.tau">[1]</a>, <a href="moose_classes.html#HHGate.tau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IntFire.tau">(IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.tau">[1]</a>, <a href="moose_classes.html#IntFire.tau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCaConc.tau">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.tau">[1]</a>, <a href="moose_classes.html#ZombieCaConc.tau">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#SynChan.tau1">tau1 (SynChan attribute)</a>, <a href="moose_builtins.html#SynChan.tau1">[1]</a>, <a href="moose_classes.html#SynChan.tau1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChan.tau2">tau2 (SynChan attribute)</a>, <a href="moose_builtins.html#SynChan.tau2">[1]</a>, <a href="moose_classes.html#SynChan.tau2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.tauD">tauD (PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.tauD">[1]</a>, <a href="moose_classes.html#PIDController.tauD">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PIDController.tauI">tauI (PIDController attribute)</a>, <a href="moose_builtins.html#PIDController.tauI">[1]</a>, <a href="moose_classes.html#PIDController.tauI">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#tauPump">tauPump()</a>, <a href="moose_builtins.html#tauPump">[1]</a>, <a href="moose_classes.html#tauPump">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#td">td</a>, <a href="moose_builtins.html#td">[1]</a>, <a href="moose_classes.html#td">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Nernst.Temperature">Temperature (Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.Temperature">[1]</a>, <a href="moose_classes.html#Nernst.Temperature">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#testSched">testSched (built-in class)</a>, <a href="moose_builtins.html#testSched">[1]</a>, <a href="moose_classes.html#testSched">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Annotator.textColor">textColor (Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.textColor">[1]</a>, <a href="moose_classes.html#Annotator.textColor">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#CaConc.thick">thick (CaConc attribute)</a>, <a href="moose_builtins.html#CaConc.thick">[1]</a>, <a href="moose_classes.html#CaConc.thick">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieCaConc.thick">(ZombieCaConc attribute)</a>, <a href="moose_builtins.html#ZombieCaConc.thick">[1]</a>, <a href="moose_classes.html#ZombieCaConc.thick">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#thickness">thickness</a>, <a href="moose_builtins.html#thickness">[1]</a>, <a href="moose_classes.html#thickness">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#PsdMesh.thickness">(PsdMesh attribute)</a>, <a href="moose_builtins.html#PsdMesh.thickness">[1]</a>, <a href="moose_classes.html#PsdMesh.thickness">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Mstring.this">this (Mstring attribute)</a>, <a href="moose_builtins.html#Mstring.this">[1]</a>, <a href="moose_classes.html#Mstring.this">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Neutral.this">(Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.this">[1]</a>, <a href="moose_classes.html#Neutral.this">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#IntFire.thresh">thresh (IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.thresh">[1]</a>, <a href="moose_classes.html#IntFire.thresh">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SpikeGen.threshold">threshold (SpikeGen attribute)</a>, <a href="moose_builtins.html#SpikeGen.threshold">[1]</a>, <a href="moose_classes.html#SpikeGen.threshold">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Table.threshold">(Table attribute)</a>, <a href="moose_builtins.html#Table.threshold">[1]</a>, <a href="moose_classes.html#Table.threshold">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ti">ti</a>, <a href="moose_builtins.html#ti">[1]</a>, <a href="moose_classes.html#ti">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.tickDt">tickDt (Clock attribute)</a>, <a href="moose_builtins.html#Clock.tickDt">[1]</a>, <a href="moose_classes.html#Clock.tickDt">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Clock.tickStep">tickStep (Clock attribute)</a>, <a href="moose_builtins.html#Clock.tickStep">[1]</a>, <a href="moose_classes.html#Clock.tickStep">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TimeTable">TimeTable (built-in class)</a>, <a href="moose_builtins.html#TimeTable">[1]</a>, <a href="moose_classes.html#TimeTable">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SteadyState.total">total (SteadyState attribute)</a>, <a href="moose_builtins.html#SteadyState.total">[1]</a>, <a href="moose_classes.html#SteadyState.total">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.totLength">totLength (CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.totLength">[1]</a>, <a href="moose_classes.html#CylMesh.totLength">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.transpose">transpose() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.transpose">[1]</a>, <a href="moose_classes.html#SparseMsg.transpose">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.trigMode">trigMode (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.trigMode">[1]</a>, <a href="moose_classes.html#PulseGen.trigMode">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.tripletFill">tripletFill() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.tripletFill">[1]</a>, <a href="moose_classes.html#SparseMsg.tripletFill">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.tweakAlpha">tweakAlpha() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.tweakAlpha">[1]</a>, <a href="moose_classes.html#HHGate.tweakAlpha">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate.tweakTau">tweakTau() (HHGate method)</a>, <a href="moose_builtins.html#HHGate.tweakTau">[1]</a>, <a href="moose_classes.html#HHGate.tweakTau">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Finfo.type">type (Finfo attribute)</a>, <a href="moose_builtins.html#Finfo.type">[1]</a>, <a href="moose_classes.html#Finfo.type">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="U">U</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.u">u (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.u">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.u">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.u0">u0 (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.u0">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.u0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SparseMsg.unsetEntry">unsetEntry() (SparseMsg method)</a>, <a href="moose_builtins.html#SparseMsg.unsetEntry">[1]</a>, <a href="moose_classes.html#SparseMsg.unsetEntry">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Unsigned">Unsigned (built-in class)</a>, <a href="moose_builtins.html#Unsigned">[1]</a>, <a href="moose_classes.html#Unsigned">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Stoich.unzombify">unzombify() (Stoich method)</a>, <a href="moose_builtins.html#Stoich.unzombify">[1]</a>, <a href="moose_classes.html#Stoich.unzombify">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Shell.useClock">useClock() (Shell method)</a>, <a href="moose_builtins.html#Shell.useClock">[1]</a>, <a href="moose_classes.html#Shell.useClock">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.useConcentration">useConcentration (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.useConcentration">[1]</a>, <a href="moose_classes.html#HHChannel.useConcentration">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ZombieHHChannel.useConcentration">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.useConcentration">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.useConcentration">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate.useInterpolation">useInterpolation (HHGate attribute)</a>, <a href="moose_builtins.html#HHGate.useInterpolation">[1]</a>, <a href="moose_classes.html#HHGate.useInterpolation">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Gsolve.useRandInit">useRandInit (Gsolve attribute)</a>, <a href="moose_builtins.html#Gsolve.useRandInit">[1]</a>, <a href="moose_classes.html#Gsolve.useRandInit">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="V">V</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#RC.V0">V0 (RC attribute)</a>, <a href="moose_builtins.html#RC.V0">[1]</a>, <a href="moose_classes.html#RC.V0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#valence">valence</a>, <a href="moose_builtins.html#valence">[1]</a>, <a href="moose_classes.html#valence">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Nernst.valence">(Nernst attribute)</a>, <a href="moose_builtins.html#Nernst.valence">[1]</a>, <a href="moose_classes.html#Nernst.valence">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#value">value</a>, <a href="moose_builtins.html#value">[1]</a>, <a href="moose_classes.html#value">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Double.value">(Double attribute)</a>, <a href="moose_builtins.html#Double.value">[1]</a>, <a href="moose_classes.html#Double.value">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Long.value">(Long attribute)</a>, <a href="moose_builtins.html#Long.value">[1]</a>, <a href="moose_classes.html#Long.value">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Mstring.value">(Mstring attribute)</a>, <a href="moose_builtins.html#Mstring.value">[1]</a>, <a href="moose_classes.html#Mstring.value">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Unsigned.value">(Unsigned attribute)</a>, <a href="moose_builtins.html#Unsigned.value">[1]</a>, <a href="moose_classes.html#Unsigned.value">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Neutral.valueFields">valueFields (Neutral attribute)</a>, <a href="moose_builtins.html#Neutral.valueFields">[1]</a>, <a href="moose_classes.html#Neutral.valueFields">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#valueOut">valueOut</a>, <a href="moose_builtins.html#valueOut">[1]</a>, <a href="moose_classes.html#valueOut">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#var">var</a>, <a href="moose_builtins.html#var">[1]</a>, <a href="moose_classes.html#var">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.varIn">varIn() (Func method)</a>, <a href="moose_builtins.html#Func.varIn">[1]</a>, <a href="moose_classes.html#Func.varIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#vars">vars</a>, <a href="moose_builtins.html#vars">[1]</a>, <a href="moose_classes.html#vars">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VClamp">VClamp (built-in class)</a>, <a href="moose_builtins.html#VClamp">[1]</a>, <a href="moose_classes.html#VClamp">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.vDiv">vDiv (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.vDiv">[1]</a>, <a href="moose_classes.html#HSolve.vDiv">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.vector">vector (TableBase attribute)</a>, <a href="moose_builtins.html#TableBase.vector">[1]</a>, <a href="moose_classes.html#TableBase.vector">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#VectorTable">VectorTable (built-in class)</a>, <a href="moose_builtins.html#VectorTable">[1]</a>, <a href="moose_classes.html#VectorTable">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.Vm">Vm (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.Vm">[1]</a>, <a href="moose_classes.html#CompartmentBase.Vm">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IntFire.Vm">(IntFire attribute)</a>, <a href="moose_builtins.html#IntFire.Vm">[1]</a>, <a href="moose_classes.html#IntFire.Vm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.Vm">(IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.Vm">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.Vm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovChannel.Vm">(MarkovChannel attribute)</a>, <a href="moose_builtins.html#MarkovChannel.Vm">[1]</a>, <a href="moose_classes.html#MarkovChannel.Vm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovRateTable.Vm">(MarkovRateTable attribute)</a>, <a href="moose_builtins.html#MarkovRateTable.Vm">[1]</a>, <a href="moose_classes.html#MarkovRateTable.Vm">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChanBase.Vm">Vm() (ChanBase method)</a>, <a href="tmp.html#ChanBase.Vm">[1]</a>, <a href="moose_builtins.html#ChanBase.Vm">[2]</a>, <a href="moose_builtins.html#ChanBase.Vm">[3]</a>, <a href="moose_classes.html#ChanBase.Vm">[4]</a>, <a href="moose_classes.html#ChanBase.Vm">[5]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#SpikeGen.Vm">(SpikeGen method)</a>, <a href="moose_builtins.html#SpikeGen.Vm">[1]</a>, <a href="moose_classes.html#SpikeGen.Vm">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#SynChanBase.Vm">(SynChanBase method)</a>, <a href="tmp.html#SynChanBase.Vm">[1]</a>, <a href="moose_builtins.html#SynChanBase.Vm">[2]</a>, <a href="moose_builtins.html#SynChanBase.Vm">[3]</a>, <a href="moose_classes.html#SynChanBase.Vm">[4]</a>, <a href="moose_classes.html#SynChanBase.Vm">[5]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Vm1">Vm1()</a>, <a href="moose_builtins.html#Vm1">[1]</a>, <a href="moose_classes.html#Vm1">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Vm2">Vm2()</a>, <a href="moose_builtins.html#Vm2">[1]</a>, <a href="moose_classes.html#Vm2">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.vMax">vMax (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.vMax">[1]</a>, <a href="moose_classes.html#HSolve.vMax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#IzhikevichNrn.Vmax">Vmax (IzhikevichNrn attribute)</a>, <a href="moose_builtins.html#IzhikevichNrn.Vmax">[1]</a>, <a href="moose_classes.html#IzhikevichNrn.Vmax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HSolve.vMin">vMin (HSolve attribute)</a>, <a href="moose_builtins.html#HSolve.vMin">[1]</a>, <a href="moose_classes.html#HSolve.vMin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.VmOut">VmOut (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.VmOut">[1]</a>, <a href="moose_classes.html#CompartmentBase.VmOut">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#IzhikevichNrn.VmOut">(IzhikevichNrn attribute)</a>, <a href="tmp.html#IzhikevichNrn.VmOut">[1]</a>, <a href="moose_builtins.html#IzhikevichNrn.VmOut">[2]</a>, <a href="moose_builtins.html#IzhikevichNrn.VmOut">[3]</a>, <a href="moose_classes.html#IzhikevichNrn.VmOut">[4]</a>, <a href="moose_classes.html#IzhikevichNrn.VmOut">[5]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#volume">volume</a>, <a href="moose_builtins.html#volume">[1]</a>, <a href="moose_classes.html#volume">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#ChemCompt.volume">(ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.volume">[1]</a>, <a href="moose_classes.html#ChemCompt.volume">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MeshEntry.volume">(MeshEntry attribute)</a>, <a href="moose_builtins.html#MeshEntry.volume">[1]</a>, <a href="moose_classes.html#MeshEntry.volume">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PoolBase.volume">(PoolBase attribute)</a>, <a href="moose_builtins.html#PoolBase.volume">[1]</a>, <a href="moose_classes.html#PoolBase.volume">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ChemCompt.voxelVolume">voxelVolume (ChemCompt attribute)</a>, <a href="moose_builtins.html#ChemCompt.voxelVolume">[1]</a>, <a href="moose_classes.html#ChemCompt.voxelVolume">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="W">W</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#Synapse.weight">weight (Synapse attribute)</a>, <a href="moose_builtins.html#Synapse.weight">[1]</a>, <a href="moose_classes.html#Synapse.weight">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#PulseGen.width">width (PulseGen attribute)</a>, <a href="moose_builtins.html#PulseGen.width">[1]</a>, <a href="moose_classes.html#PulseGen.width">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#PulseGen.widthIn">widthIn() (PulseGen method)</a>, <a href="moose_builtins.html#PulseGen.widthIn">[1]</a>, <a href="moose_classes.html#PulseGen.widthIn">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="X">X</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#x">x</a>, <a href="moose_builtins.html#x">[1]</a>, <a href="moose_classes.html#x">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Annotator.x">(Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.x">[1]</a>, <a href="moose_classes.html#Annotator.x">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.x">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.x">[1]</a>, <a href="moose_classes.html#CompartmentBase.x">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel.X">X (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.X">[1]</a>, <a href="moose_classes.html#HHChannel.X">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.X">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.X">[1]</a>, <a href="moose_classes.html#HHChannel2D.X">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.X">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.X">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.X">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CompartmentBase.x0">x0 (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.x0">[1]</a>, <a href="moose_classes.html#CompartmentBase.x0">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CubeMesh.x0">(CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.x0">[1]</a>, <a href="moose_classes.html#CubeMesh.x0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.x0">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.x0">[1]</a>, <a href="moose_classes.html#CylMesh.x0">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.x1">x1 (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.x1">[1]</a>, <a href="moose_classes.html#CubeMesh.x1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.x1">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.x1">[1]</a>, <a href="moose_classes.html#CylMesh.x1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.xdivs">xdivs (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.xdivs">[1]</a>, <a href="moose_classes.html#Interpol2D.xdivs">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.xdivs">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.xdivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.xdivs">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.xdivs">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.xdivs">[1]</a>, <a href="moose_classes.html#VectorTable.xdivs">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.xdivsA">xdivsA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xdivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.xdivsA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.xdivsB">xdivsB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xdivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.xdivsB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Func.xIn">xIn() (Func method)</a>, <a href="moose_builtins.html#Func.xIn">[1]</a>, <a href="moose_classes.html#Func.xIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.Xindex">Xindex (HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Xindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.Xindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.xmax">xmax (Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.xmax">[1]</a>, <a href="moose_classes.html#Interpol.xmax">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.xmax">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.xmax">[1]</a>, <a href="moose_classes.html#Interpol2D.xmax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.xmax">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.xmax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.xmax">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.xmax">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.xmax">[1]</a>, <a href="moose_classes.html#VectorTable.xmax">[2]</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#HHGate2D.xmaxA">xmaxA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xmaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.xmaxA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.xmaxB">xmaxB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xmaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.xmaxB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol.xmin">xmin (Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.xmin">[1]</a>, <a href="moose_classes.html#Interpol.xmin">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Interpol2D.xmin">(Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.xmin">[1]</a>, <a href="moose_classes.html#Interpol2D.xmin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MarkovSolverBase.xmin">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.xmin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.xmin">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#VectorTable.xmin">(VectorTable attribute)</a>, <a href="moose_builtins.html#VectorTable.xmin">[1]</a>, <a href="moose_classes.html#VectorTable.xmin">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.xminA">xminA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xminA">[1]</a>, <a href="moose_classes.html#HHGate2D.xminA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.xminB">xminB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.xminB">[1]</a>, <a href="moose_classes.html#HHGate2D.xminB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#TableBase.xplot">xplot() (TableBase method)</a>, <a href="moose_builtins.html#TableBase.xplot">[1]</a>, <a href="moose_classes.html#TableBase.xplot">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.Xpower">Xpower (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Xpower">[1]</a>, <a href="moose_classes.html#HHChannel.Xpower">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.Xpower">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Xpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.Xpower">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.Xpower">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Xpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Xpower">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#xyIn">xyIn()</a>, <a href="moose_builtins.html#xyIn">[1]</a>, <a href="moose_classes.html#xyIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#xyzIn">xyzIn()</a>, <a href="moose_builtins.html#xyzIn">[1]</a>, <a href="moose_classes.html#xyzIn">[2]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="Y">Y</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#y">y</a>, <a href="moose_builtins.html#y">[1]</a>, <a href="moose_classes.html#y">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Annotator.y">(Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.y">[1]</a>, <a href="moose_classes.html#Annotator.y">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.y">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.y">[1]</a>, <a href="moose_classes.html#CompartmentBase.y">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel.Y">Y (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Y">[1]</a>, <a href="moose_classes.html#HHChannel.Y">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.Y">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Y">[1]</a>, <a href="moose_classes.html#HHChannel2D.Y">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol.y">y (Interpol attribute)</a>, <a href="moose_builtins.html#Interpol.y">[1]</a>, <a href="moose_classes.html#Interpol.y">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#TableBase.y">(TableBase attribute)</a>, <a href="moose_builtins.html#TableBase.y">[1]</a>, <a href="moose_classes.html#TableBase.y">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#ZombieHHChannel.Y">Y (ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Y">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Y">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.y0">y0 (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.y0">[1]</a>, <a href="moose_classes.html#CompartmentBase.y0">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CubeMesh.y0">(CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.y0">[1]</a>, <a href="moose_classes.html#CubeMesh.y0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.y0">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.y0">[1]</a>, <a href="moose_classes.html#CylMesh.y0">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.y1">y1 (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.y1">[1]</a>, <a href="moose_classes.html#CubeMesh.y1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.y1">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.y1">[1]</a>, <a href="moose_classes.html#CylMesh.y1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.ydivs">ydivs (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.ydivs">[1]</a>, <a href="moose_classes.html#Interpol2D.ydivs">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.ydivs">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.ydivs">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.ydivs">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.ydivsA">ydivsA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.ydivsA">[1]</a>, <a href="moose_classes.html#HHGate2D.ydivsA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.ydivsB">ydivsB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.ydivsB">[1]</a>, <a href="moose_classes.html#HHGate2D.ydivsB">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#yIn">yIn()</a>, <a href="moose_builtins.html#yIn">[1]</a>, <a href="moose_classes.html#yIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.Yindex">Yindex (HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Yindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.Yindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.ymax">ymax (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.ymax">[1]</a>, <a href="moose_classes.html#Interpol2D.ymax">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.ymax">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.ymax">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.ymax">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.ymaxA">ymaxA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.ymaxA">[1]</a>, <a href="moose_classes.html#HHGate2D.ymaxA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.ymaxB">ymaxB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.ymaxB">[1]</a>, <a href="moose_classes.html#HHGate2D.ymaxB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#Interpol2D.ymin">ymin (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.ymin">[1]</a>, <a href="moose_classes.html#Interpol2D.ymin">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#MarkovSolverBase.ymin">(MarkovSolverBase attribute)</a>, <a href="moose_builtins.html#MarkovSolverBase.ymin">[1]</a>, <a href="moose_classes.html#MarkovSolverBase.ymin">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHGate2D.yminA">yminA (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.yminA">[1]</a>, <a href="moose_classes.html#HHGate2D.yminA">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHGate2D.yminB">yminB (HHGate2D attribute)</a>, <a href="moose_builtins.html#HHGate2D.yminB">[1]</a>, <a href="moose_classes.html#HHGate2D.yminB">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.Ypower">Ypower (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Ypower">[1]</a>, <a href="moose_classes.html#HHChannel.Ypower">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.Ypower">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Ypower">[1]</a>, <a href="moose_classes.html#HHChannel2D.Ypower">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.Ypower">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Ypower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Ypower">[2]</a>
- </dt>
-
- </dl></dd>
- </dl></td>
-</tr></table>
-
-<h2 id="Z">Z</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#z">z</a>, <a href="moose_builtins.html#z">[1]</a>, <a href="moose_classes.html#z">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#Annotator.z">(Annotator attribute)</a>, <a href="moose_builtins.html#Annotator.z">[1]</a>, <a href="moose_classes.html#Annotator.z">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.z">(CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.z">[1]</a>, <a href="moose_classes.html#CompartmentBase.z">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#HHChannel.Z">Z (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Z">[1]</a>, <a href="moose_classes.html#HHChannel.Z">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.Z">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Z">[1]</a>, <a href="moose_classes.html#HHChannel2D.Z">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#Interpol2D.z">z (Interpol2D attribute)</a>, <a href="moose_builtins.html#Interpol2D.z">[1]</a>, <a href="moose_classes.html#Interpol2D.z">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.Z">Z (ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Z">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Z">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CompartmentBase.z0">z0 (CompartmentBase attribute)</a>, <a href="moose_builtins.html#CompartmentBase.z0">[1]</a>, <a href="moose_classes.html#CompartmentBase.z0">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CubeMesh.z0">(CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.z0">[1]</a>, <a href="moose_classes.html#CubeMesh.z0">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#CylMesh.z0">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.z0">[1]</a>, <a href="moose_classes.html#CylMesh.z0">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#CubeMesh.z1">z1 (CubeMesh attribute)</a>, <a href="moose_builtins.html#CubeMesh.z1">[1]</a>, <a href="moose_classes.html#CubeMesh.z1">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#CylMesh.z1">(CylMesh attribute)</a>, <a href="moose_builtins.html#CylMesh.z1">[1]</a>, <a href="moose_classes.html#CylMesh.z1">[2]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="tmp.html#zIn">zIn()</a>, <a href="moose_builtins.html#zIn">[1]</a>, <a href="moose_classes.html#zIn">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel2D.Zindex">Zindex (HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Zindex">[1]</a>, <a href="moose_classes.html#HHChannel2D.Zindex">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#MgBlock.Zk">Zk (MgBlock attribute)</a>, <a href="moose_builtins.html#MgBlock.Zk">[1]</a>, <a href="moose_classes.html#MgBlock.Zk">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieBufPool">ZombieBufPool (built-in class)</a>, <a href="moose_builtins.html#ZombieBufPool">[1]</a>, <a href="moose_classes.html#ZombieBufPool">[2]</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="tmp.html#ZombieCaConc">ZombieCaConc (built-in class)</a>, <a href="moose_builtins.html#ZombieCaConc">[1]</a>, <a href="moose_classes.html#ZombieCaConc">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieCompartment">ZombieCompartment (built-in class)</a>, <a href="moose_builtins.html#ZombieCompartment">[1]</a>, <a href="moose_classes.html#ZombieCompartment">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieEnz">ZombieEnz (built-in class)</a>, <a href="moose_builtins.html#ZombieEnz">[1]</a>, <a href="moose_classes.html#ZombieEnz">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieFuncPool">ZombieFuncPool (built-in class)</a>, <a href="moose_builtins.html#ZombieFuncPool">[1]</a>, <a href="moose_classes.html#ZombieFuncPool">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel">ZombieHHChannel (built-in class)</a>, <a href="moose_builtins.html#ZombieHHChannel">[1]</a>, <a href="moose_classes.html#ZombieHHChannel">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieMMenz">ZombieMMenz (built-in class)</a>, <a href="moose_builtins.html#ZombieMMenz">[1]</a>, <a href="moose_classes.html#ZombieMMenz">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombiePool">ZombiePool (built-in class)</a>, <a href="moose_builtins.html#ZombiePool">[1]</a>, <a href="moose_classes.html#ZombiePool">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieReac">ZombieReac (built-in class)</a>, <a href="moose_builtins.html#ZombieReac">[1]</a>, <a href="moose_classes.html#ZombieReac">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#HHChannel.Zpower">Zpower (HHChannel attribute)</a>, <a href="moose_builtins.html#HHChannel.Zpower">[1]</a>, <a href="moose_classes.html#HHChannel.Zpower">[2]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="tmp.html#HHChannel2D.Zpower">(HHChannel2D attribute)</a>, <a href="moose_builtins.html#HHChannel2D.Zpower">[1]</a>, <a href="moose_classes.html#HHChannel2D.Zpower">[2]</a>
- </dt>
-
-
- <dt><a href="tmp.html#ZombieHHChannel.Zpower">(ZombieHHChannel attribute)</a>, <a href="moose_builtins.html#ZombieHHChannel.Zpower">[1]</a>, <a href="moose_classes.html#ZombieHHChannel.Zpower">[2]</a>
- </dt>
-
- </dl></dd>
- </dl></td>
-</tr></table>
-
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- <img class="logo" src="_static/moose_logo.png" alt="Logo"/>
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- <h3>Quick search</h3>
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- Enter search terms or a module, class or function name.
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- © Copyright 2014, Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray and Dilawar Singh.
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- accesskey="N">next</a> |</li>
- <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li>
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- <div class="section" id="the-multiscale-object-oriented-simulation-environment">
-<h1>the Multiscale Object-Oriented Simulation Environment<a class="headerlink" href="#the-multiscale-object-oriented-simulation-environment" title="Permalink to this headline">¶</a></h1>
-<p>Contents:</p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="moose_overview.html">MOOSE = Multiscale Object Oriented Simulation Environment.</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#how-to-use-the-documentation">How to use the documentation</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="moose_overview.html#brief-overview-of-pymoose">Brief overview of PyMOOSE</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#vec">vec</a></li>
-<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#melement">melement</a></li>
-<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#creating-melements">Creating melements</a></li>
-<li class="toctree-l2"><a class="reference internal" href="moose_overview.html#module-functions">module functions</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="moose_builtins.html">MOOSE Builtins</a></li>
-<li class="toctree-l1"><a class="reference internal" href="moose_classes.html">MOOSE Classes</a></li>
-</ul>
-</div>
-</div>
-<div class="section" id="indices-and-tables">
-<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="genindex.html"><em>Index</em></a></li>
-<li><a class="reference internal" href="py-modindex.html"><em>Module Index</em></a></li>
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- <ul>
-<li><a class="reference internal" href="#">the Multiscale Object-Oriented Simulation Environment</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
-</ul>
-
- <h4>Next topic</h4>
- <p class="topless"><a href="moose_overview.html"
- title="next chapter">MOOSE = Multiscale Object Oriented Simulation Environment.</a></p>
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- <ul class="this-page-menu">
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+++ /dev/null
@@ -1,889 +0,0 @@
-
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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- >modules</a> |</li>
- <li class="right" >
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- accesskey="N">next</a> |</li>
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-
- <div class="section" id="module-moose">
-<span id="moose-builtins"></span><h1>MOOSE builtins<a class="headerlink" href="#module-moose" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="moose-multiscale-object-oriented-simulation-environment">
-<h2>MOOSE = Multiscale Object Oriented Simulation Environment.<a class="headerlink" href="#moose-multiscale-object-oriented-simulation-environment" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="how-to-use-the-documentation">
-<h3>How to use the documentation<a class="headerlink" href="#how-to-use-the-documentation" title="Permalink to this headline">¶</a></h3>
-<p>MOOSE documentation is split into Python documentation and builtin
-documentation. The functions and classes that are only part of the
-Python interface can be viewed via Python’s builtin <tt class="docutils literal"><span class="pre">help</span></tt>
-function:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">help</span><span class="p">(</span><span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>...</p>
-<p>The documentation built into main C++ code of MOOSE can be accessed
-via the module function <tt class="docutils literal"><span class="pre">doc</span></tt>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">moose</span><span class="o">.</span><span class="n">doc</span><span class="p">(</span><span class="s">'Neutral'</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>...</p>
-<p>To get documentation about a particular field:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">moose</span><span class="o">.</span><span class="n">doc</span><span class="p">(</span><span class="s">'Neutral.childMsg'</span><span class="p">)</span>
-</pre></div>
-</div>
-</div>
-</div>
-<div class="section" id="brief-overview-of-pymoose">
-<h2>Brief overview of PyMOOSE<a class="headerlink" href="#brief-overview-of-pymoose" title="Permalink to this headline">¶</a></h2>
-<p>Classes:</p>
-<div class="section" id="vec">
-<h3>vec<a class="headerlink" href="#vec" title="Permalink to this headline">¶</a></h3>
-<p>this is the unique identifier of a MOOSE object. Note that you can
-create multiple references to the same MOOSE object in Python, but as
-long as they have the same path/id value, they all point to the same
-entity in MOOSE.</p>
-<p>Constructor:</p>
-<p>You can create a new vec using the constructor:</p>
-<p>vec(path, dimension, classname)</p>
-<p>Fields:</p>
-<p>value – unsigned integer representation of id of this vec</p>
-<p>path – string representing the path corresponding this vec</p>
-<p>shape – tuple containing the dimensions of this vec</p>
-<p>Apart from these, every vec exposes the fields of all its elements
-in a vectorized form. For example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">iaf</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">vec</span><span class="p">(</span><span class="s">'/iaf'</span><span class="p">,</span> <span class="p">(</span><span class="mi">10</span><span class="p">),</span> <span class="s">'IntFire'</span><span class="p">)</span>
-<span class="gp">>>> </span><span class="n">iaf</span><span class="o">.</span><span class="n">Vm</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
-<span class="gp">>>> </span><span class="k">print</span> <span class="n">iaf</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">Vm</span>
-<span class="go">5.0</span>
-<span class="gp">>>> </span><span class="k">print</span> <span class="n">iaf</span><span class="o">.</span><span class="n">Vm</span>
-<span class="go">array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])</span>
-</pre></div>
-</div>
-<p>Methods:</p>
-<p>vec implements part of the sequence protocol:</p>
-<p>len(em) – the first dimension of em.</p>
-<p>em[n] – the n-th element in em.</p>
-<p>em[n1:n2] – a tuple containing n1 to n2-th (exclusive) element in em.</p>
-<p>elem in em – True if elem is contained in em.</p>
-</div>
-<div class="section" id="melement">
-<h3>melement<a class="headerlink" href="#melement" title="Permalink to this headline">¶</a></h3>
-<p>Single moose object. It has three numbers to uniquely identify it:</p>
-<p>id - id of the vec containing this element</p>
-<p>dataIndex - index of this element in the container vec</p>
-<p>fieldIndex - if this is a tertiary object, i.e. acts
-as a field in another element (like synapse[0] in IntFire[1]), then
-the index of this field in the containing element.</p>
-<p>Methods:</p>
-<p>getId – vec object containing this element.
-vec() – vec object containing this element.</p>
-<p>getDataIndex() – unsigned integer representing the index of this
-element in containing MOOSE object.</p>
-<p>getFieldIndex() – unsigned integer representing the index of this
-element as a field in the containing Element.</p>
-<p>getFieldType(field) – human readable datatype information of field</p>
-<p>getField(field) – get value of field</p>
-<p>setField(field, value) – assign value to field</p>
-<p>getFieldNames(fieldType) – tuple containing names of all the fields
-of type fieldType. fieldType can be valueFinfo, lookupFinfo, srcFinfo,
-destFinfo and sharedFinfo. If nothing is passed, a union of all of the
-above is used and all the fields are returned.</p>
-<p>connect(srcField, destObj, destField, msgType) – connect srcField of
-this element to destField of destObj.</p>
-<p>melement is something like an abstract base class in C++. The concrete
-base class is Neutral. However you do not need to cast objects down to
-access their fields. The PyMOOSE interface will automatically do the
-check for you and raise an exception if the specified field does not
-exist for the current element.</p>
-</div>
-<div class="section" id="creating-melements">
-<h3>Creating melements<a class="headerlink" href="#creating-melements" title="Permalink to this headline">¶</a></h3>
-<p>To create the objects of concrete subclasses of melement, the class
-can be called as follows:</p>
-<p>melement(path, dims, dtype, parent)</p>
-<p>path: This is like unix filesystem path and is the concatenation of
-name of the element to be created and that of all its ancestors
-spearated by <cite>/</cite>. For example, path=`/a/b` will create the element
-named <cite>b</cite> under element <cite>a</cite>. Note that if <cite>a</cite> does not exist, this
-will raise an error. However, if <cite>parent</cite> is specified, <cite>path</cite> should
-contain only the name of the element.</p>
-<p>dims: (optional) tuple specifying the dimension of the containing melement to be
-created. It is (1,) by default.</p>
-<p>dtype: string specifying the class name of the element to be created.</p>
-<p>parent: (optional) string specifying the path of the parent element or
-the Id or the ObjId of the parent element or a reference to the parent
-element. If this is specified, the first argument <cite>path</cite> is treated as
-the name of the element to be created.</p>
-<p>All arguments can be passed as keyword arguments.</p>
-<p>For concrete subclasses of melement, you do not need to pass the class
-argument because the class name is passed automatically to <cite>melement</cite>
-__init__ method.</p>
-<p>a = Neutral(‘alpha’) # Creates element named <cite>alpha</cite> under current working element
-b = Neutral(‘alpha/beta’) # Creates the element named <cite>beta</cite> under <cite>alpha</cite>
-c = Cell(‘charlie’, parent=a) # creates element <cite>charlie</cite> under <cite>alpha</cite>
-d = DiffAmp(‘delta’, parent=’alpha/beta’) # creates element <cite>delta</cite> under <cite>beta</cite></p>
-</div>
-<div class="section" id="module-functions">
-<h3>module functions<a class="headerlink" href="#module-functions" title="Permalink to this headline">¶</a></h3>
-<p>element(path) - returns a reference to an existing object converted to
-the right class. Raises ValueError if path does not exist.</p>
-<p>copy(src=<src>, dest=<dest>, name=<name_of_the_copy>, n=<num_copies>,
-copyMsg=<whether_to_copy_messages) – make a copy of source object as
-a child of the destination object.</p>
-<p>move(src, dest) – move src object under dest object.</p>
-<p>useClock(tick, path, update_function) – schedule <update_function> of
-every object that matches <path> on clock no. <tick>. Most commonly
-the function is ‘process’. NOTE: unlike earlier versions, now
-autoschedule is not available. You have to call useClock for every
-element that should be updated during the simulation.</p>
-<p>The sequence of clockticks with the same dt is according to their
-number. This is utilized for controlling the order of updates in
-various objects where it matters.</p>
-<p>The following convention should be observed when assigning clockticks
-to various components of a model:</p>
-<p>Clock ticks 0-3 are for electrical (biophysical) components, 4 and 5
-are for chemical kinetics, 6 and 7 are for lookup tables and stimulus,
-8 and 9 are for recording tables.</p>
-<p>Generally, ‘process’ is the method to be assigned a clock
-tick. Notable exception is ‘init’ method of Compartment class which is
-assigned tick 0.</p>
-<p>0 : Compartment: ‘init’
-1 : Compartment: ‘process’
-2 : HHChannel and other channels: ‘process’
-3 : CaConc : ‘process’
-4,5 : Elements for chemical kinetics : ‘process’
-6,7 : Lookup (tables), stimulus : ‘process’
-8,9 : Tables for plotting : process</p>
-<p>Example:
-moose.useClock(0, ‘/model/compartment_1’, ‘init’)
-moose.useClock(1, ‘/model/compartment_1’, ‘process’)</p>
-<p>setClock(tick, dt) – set dt of clock no <tick>.</p>
-<p>start(runtime) – start simulation of <runtime> time.</p>
-<p>reinit() – reinitialize simulation.</p>
-<p>stop() – stop simulation</p>
-<p>isRunning() – true if simulation is in progress, false otherwise.</p>
-<p>exists(path) – true if there is a pre-existing object with the specified path.</p>
-<p>loadModel(filepath, modelpath) – load file in <filepath> into node
-<modelpath> of the moose model-tree.</p>
-<p>setCwe(obj) – set the current working element to <obj> - which can be
-either a string representing the path of the object in the moose
-model-tree, or an vec.
-ce(obj) – an alias for setCwe.</p>
-<p>getCwe() – returns vec containing the current working element.
-pwe() – an alias for getCwe.</p>
-<p>showfields(obj) – print the fields in object in human readable format</p>
-<p>le(obj) – list element under object, if no parameter specified, list
-elements under current working element</p>
-<dl class="function">
-<dt id="moose.pwe">
-<tt class="descclassname">moose.</tt><tt class="descname">pwe</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.pwe" title="Permalink to this definition">¶</a></dt>
-<dd><p>Print present working element. Convenience function for GENESIS
-users. If you want to retrieve the element in stead of printing
-the path, use moose.getCwe()</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.le">
-<tt class="descclassname">moose.</tt><tt class="descname">le</tt><big>(</big><em>el=None</em><big>)</big><a class="headerlink" href="#moose.le" title="Permalink to this definition">¶</a></dt>
-<dd><p>List elements under <cite>el</cite> or current element if no argument
-specified.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>el</strong> : str/melement/vec/None</p>
-<blockquote>
-<div><dl class="docutils">
-<dt>The element or the path under which to look. If <cite>None</cite>, children</dt>
-<dd><p class="first last">of current working element are displayed.</p>
-</dd>
-</dl>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.ce">
-<tt class="descclassname">moose.</tt><tt class="descname">ce</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.ce" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the current working element. ‘ce’ is an alias of this function</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.showfield">
-<tt class="descclassname">moose.</tt><tt class="descname">showfield</tt><big>(</big><em>el</em>, <em>field='*'</em>, <em>showtype=False</em><big>)</big><a class="headerlink" href="#moose.showfield" title="Permalink to this definition">¶</a></dt>
-<dd><p>Show the fields of the element <cite>el</cite>, their data types and
-values in human readable format. Convenience function for GENESIS
-users.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>el</strong> : melement/str</p>
-<blockquote>
-<div><p>Element or path of an existing element.</p>
-</div></blockquote>
-<p><strong>field</strong> : str</p>
-<blockquote>
-<div><p>Field to be displayed. If ‘*’ (default), all fields are displayed.</p>
-</div></blockquote>
-<p><strong>showtype</strong> : bool</p>
-<blockquote>
-<div><p>If True show the data type of each field. False by default.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.showmsg">
-<tt class="descclassname">moose.</tt><tt class="descname">showmsg</tt><big>(</big><em>el</em><big>)</big><a class="headerlink" href="#moose.showmsg" title="Permalink to this definition">¶</a></dt>
-<dd><p>Print the incoming and outgoing messages of <cite>el</cite>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>el</strong> : melement/vec/str</p>
-<blockquote>
-<div><p>Object whose messages are to be displayed.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.doc">
-<tt class="descclassname">moose.</tt><tt class="descname">doc</tt><big>(</big><em>arg</em>, <em>inherited=True</em>, <em>paged=True</em><big>)</big><a class="headerlink" href="#moose.doc" title="Permalink to this definition">¶</a></dt>
-<dd><p>Display the documentation for class or field in a class.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>arg</strong> : str/class/melement/vec</p>
-<blockquote>
-<div><p>A string specifying a moose class name and a field name
-separated by a dot. e.g., ‘Neutral.name’. Prepending <cite>moose.</cite>
-is allowed. Thus moose.doc(‘moose.Neutral.name’) is equivalent
-to the above.
-It can also be string specifying just a moose class name or a
-moose class or a moose object (instance of melement or vec
-or there subclasses). In that case, the builtin documentation
-for the corresponding moose class is displayed.</p>
-</div></blockquote>
-<p><strong>paged: bool</strong></p>
-<blockquote>
-<div><p>Whether to display the docs via builtin pager or print and
-exit. If not specified, it defaults to False and
-moose.doc(xyz) will print help on xyz and return control to
-command line.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">None</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises :</th><td class="field-body"><p class="first"><strong>NameError</strong></p>
-<blockquote class="last">
-<div><p>If class or field does not exist.</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.element">
-<tt class="descclassname">moose.</tt><tt class="descname">element</tt><big>(</big><em>arg</em><big>)</big> → moose object<a class="headerlink" href="#moose.element" title="Permalink to this definition">¶</a></dt>
-<dd><p>Convert a path or an object to the appropriate builtin moose class
-instance</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>arg</strong> : str/vec/moose object</p>
-<blockquote>
-<div><p>path of the moose element to be converted or another element (possibly
-available as a superclass instance).</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">melement</p>
-<blockquote class="last">
-<div><p>MOOSE element (object) corresponding to the <cite>arg</cite> converted to write subclass.</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.getFieldNames">
-<tt class="descclassname">moose.</tt><tt class="descname">getFieldNames</tt><big>(</big><em>className</em>, <em>finfoType='valueFinfo'</em><big>)</big> → tuple<a class="headerlink" href="#moose.getFieldNames" title="Permalink to this definition">¶</a></dt>
-<dd><p>Get a tuple containing the name of all the fields of <cite>finfoType</cite>
-kind.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>className</strong> : string</p>
-<blockquote>
-<div><p>Name of the class to look up.</p>
-</div></blockquote>
-<p><strong>finfoType</strong> : string</p>
-<blockquote>
-<div><p>The kind of field (<cite>valueFinfo</cite>, <cite>srcFinfo</cite>, <cite>destFinfo</cite>,
-<cite>lookupFinfo</cite>, <cite>fieldElementFinfo</cite>.).</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">tuple</p>
-<blockquote class="last">
-<div><p>Names of the fields of type <cite>finfoType</cite> in class <cite>className</cite>.</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.copy">
-<tt class="descclassname">moose.</tt><tt class="descname">copy</tt><big>(</big><em>src</em>, <em>dest</em>, <em>name</em>, <em>n</em>, <em>toGlobal</em>, <em>copyExtMsg</em><big>)</big> → bool<a class="headerlink" href="#moose.copy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Make copies of a moose object.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>src</strong> : vec, element or str</p>
-<blockquote>
-<div><p>source object.</p>
-</div></blockquote>
-<p><strong>dest</strong> : vec, element or str</p>
-<blockquote>
-<div><p>Destination object to copy into.</p>
-</div></blockquote>
-<p><strong>name</strong> : str</p>
-<blockquote>
-<div><p>Name of the new object. If omitted, name of the original will be used.</p>
-</div></blockquote>
-<p><strong>n</strong> : int</p>
-<blockquote>
-<div><p>Number of copies to make.</p>
-</div></blockquote>
-<p><strong>toGlobal</strong> : int</p>
-<blockquote>
-<div><p>Relevant for parallel environments only. If false, the copies will
-reside on local node, otherwise all nodes get the copies.</p>
-</div></blockquote>
-<p><strong>copyExtMsg</strong> : int</p>
-<blockquote>
-<div><p>If true, messages to/from external objects are also copied.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">vec</p>
-<blockquote class="last">
-<div><p>newly copied vec</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.move">
-<tt class="descclassname">moose.</tt><tt class="descname">move</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.move" title="Permalink to this definition">¶</a></dt>
-<dd><p>Move a vec object to a destination.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.delete">
-<tt class="descclassname">moose.</tt><tt class="descname">delete</tt><big>(</big><em>obj</em><big>)</big> → None<a class="headerlink" href="#moose.delete" title="Permalink to this definition">¶</a></dt>
-<dd><p>Delete the underlying moose object. This does not delete any of the
-Python objects referring to this vec but does invalidate them. Any
-attempt to access them will raise a ValueError.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>id</strong> : vec</p>
-<blockquote>
-<div><p>vec of the object to be deleted.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.useClock">
-<tt class="descclassname">moose.</tt><tt class="descname">useClock</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.useClock" title="Permalink to this definition">¶</a></dt>
-<dd><p>Schedule objects on a specified clock</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.setClock">
-<tt class="descclassname">moose.</tt><tt class="descname">setClock</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.setClock" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the dt of a clock.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.start">
-<tt class="descclassname">moose.</tt><tt class="descname">start</tt><big>(</big><em>time</em><big>)</big> → None<a class="headerlink" href="#moose.start" title="Permalink to this definition">¶</a></dt>
-<dd><p>Run simulation for <cite>t</cite> time. Advances the simulator clock by <cite>t</cite>
-time.</p>
-<p>After setting up a simulation, YOU MUST CALL MOOSE.REINIT() before
-CALLING MOOSE.START() TO EXECUTE THE SIMULATION. Otherwise, the
-simulator behaviour will be undefined. Once moose.reinit() has been
-called, you can call moose.start(t) as many time as you like. This
-will continue the simulation from the last state for <cite>t</cite> time.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>t</strong> : float</p>
-<blockquote>
-<div><p>duration of simulation.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p>
-</td>
-</tr>
-</tbody>
-</table>
-<div class="admonition-see-also admonition seealso">
-<p class="first admonition-title">See also</p>
-<dl class="last docutils">
-<dt><a class="reference internal" href="#moose.reinit" title="moose.reinit"><tt class="xref py py-obj docutils literal"><span class="pre">moose.reinit</span></tt></a></dt>
-<dd>(Re)initialize simulation</dd>
-</dl>
-</div>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.reinit">
-<tt class="descclassname">moose.</tt><tt class="descname">reinit</tt><big>(</big><big>)</big> → None<a class="headerlink" href="#moose.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>Reinitialize simulation.</p>
-<p>This function (re)initializes moose simulation. It must be called
-before you start the simulation (see moose.start). If you want to
-continue simulation after you have called moose.reinit() and
-moose.start(), you must NOT call moose.reinit() again. Calling
-moose.reinit() again will take the system back to initial setting
-(like clear out all data recording tables, set state variables to
-their initial values, etc.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.stop">
-<tt class="descclassname">moose.</tt><tt class="descname">stop</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.stop" title="Permalink to this definition">¶</a></dt>
-<dd><p>Stop simulation</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.isRunning">
-<tt class="descclassname">moose.</tt><tt class="descname">isRunning</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.isRunning" title="Permalink to this definition">¶</a></dt>
-<dd><p>True if the simulation is currently running.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.exists">
-<tt class="descclassname">moose.</tt><tt class="descname">exists</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.exists" title="Permalink to this definition">¶</a></dt>
-<dd><p>True if there is an object with specified path.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.writeSBML">
-<tt class="descclassname">moose.</tt><tt class="descname">writeSBML</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.writeSBML" title="Permalink to this definition">¶</a></dt>
-<dd><p>Export biochemical model to an SBML file.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.readSBML">
-<tt class="descclassname">moose.</tt><tt class="descname">readSBML</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.readSBML" title="Permalink to this definition">¶</a></dt>
-<dd><p>Import SBML model to Moose.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.loadModel">
-<tt class="descclassname">moose.</tt><tt class="descname">loadModel</tt><big>(</big><em>filename</em>, <em>modelpath</em>, <em>solverclass</em><big>)</big> → vec<a class="headerlink" href="#moose.loadModel" title="Permalink to this definition">¶</a></dt>
-<dd><p>Load model from a file to a specified path.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>filename</strong> : str</p>
-<blockquote>
-<div><p>model description file.</p>
-</div></blockquote>
-<p><strong>modelpath</strong> : str</p>
-<blockquote>
-<div><p>moose path for the top level element of the model to be created.</p>
-</div></blockquote>
-<p><strong>solverclass</strong> : str, optional</p>
-<blockquote>
-<div><p>solver type to be used for simulating the model.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">vec</p>
-<blockquote class="last">
-<div><p>loaded model container vec.</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.saveModel">
-<tt class="descclassname">moose.</tt><tt class="descname">saveModel</tt><big>(</big><em>source</em>, <em>filename</em><big>)</big> → None<a class="headerlink" href="#moose.saveModel" title="Permalink to this definition">¶</a></dt>
-<dd><p>Save model rooted at <cite>source</cite> to file <cite>filename</cite>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>source</strong> : vec/element/str</p>
-<blockquote>
-<div><p>root of the model tree</p>
-</div></blockquote>
-<p><strong>filename</strong> : str</p>
-<blockquote>
-<div><p>destination file to save the model in.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.connect">
-<tt class="descclassname">moose.</tt><tt class="descname">connect</tt><big>(</big><em>src</em>, <em>src_field</em>, <em>dest</em>, <em>dest_field</em>, <em>message_type</em><big>)</big> → bool<a class="headerlink" href="#moose.connect" title="Permalink to this definition">¶</a></dt>
-<dd><p>Create a message between <cite>src_field</cite> on <cite>src</cite> object to <cite>dest_field</cite>
-on <cite>dest</cite> object.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>src</strong> : element/vec/string</p>
-<blockquote>
-<div><p>the source object (or its path)</p>
-</div></blockquote>
-<p><strong>src_field</strong> : str</p>
-<blockquote>
-<div><p>the source field name. Fields listed under <cite>srcFinfo</cite> and
-<cite>sharedFinfo</cite> qualify for this.</p>
-</div></blockquote>
-<p><strong>dest</strong> : element/vec/string</p>
-<blockquote>
-<div><p>the destination object.</p>
-</div></blockquote>
-<p><strong>dest_field</strong> : str</p>
-<blockquote>
-<div><p>the destination field name. Fields listed under <cite>destFinfo</cite>
-and <cite>sharedFinfo</cite> qualify for this.</p>
-</div></blockquote>
-<p><strong>message_type</strong> : str (optional)</p>
-<blockquote>
-<div><p>Type of the message. Can be <cite>Single</cite>, <cite>OneToOne</cite>, <cite>OneToAll</cite>.
-If not specified, it defaults to <cite>Single</cite>.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">melement</p>
-<blockquote class="last">
-<div><p>message-manager for the newly created message.</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.getCwe">
-<tt class="descclassname">moose.</tt><tt class="descname">getCwe</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.getCwe" title="Permalink to this definition">¶</a></dt>
-<dd><p>Get the current working element. ‘pwe’ is an alias of this function.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.setCwe">
-<tt class="descclassname">moose.</tt><tt class="descname">setCwe</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.setCwe" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set the current working element. ‘ce’ is an alias of this function</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.getFieldDict">
-<tt class="descclassname">moose.</tt><tt class="descname">getFieldDict</tt><big>(</big><em>className</em>, <em>finfoType</em><big>)</big> → dict<a class="headerlink" href="#moose.getFieldDict" title="Permalink to this definition">¶</a></dt>
-<dd><p>Get dictionary of field names and types for specified class.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>className</strong> : str</p>
-<blockquote>
-<div><p>MOOSE class to find the fields of.</p>
-</div></blockquote>
-<p><strong>finfoType</strong> : str (optional)</p>
-<blockquote>
-<div><p>Finfo type of the fields to find. If empty or not specified, all
-fields will be retrieved.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">dict</p>
-<blockquote class="last">
-<div><p>field names and their types.</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-<p class="rubric">Notes</p>
-<p>This behaviour is different from <cite>getFieldNames</cite> where only
-<cite>valueFinfo`s are returned when `finfoType</cite> remains unspecified.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.getField">
-<tt class="descclassname">moose.</tt><tt class="descname">getField</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.getField" title="Permalink to this definition">¶</a></dt>
-<dd><p>getField(element, field, fieldtype) – Get specified field of specified type from object vec.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.seed">
-<tt class="descclassname">moose.</tt><tt class="descname">seed</tt><big>(</big><em>seedvalue</em><big>)</big> → None<a class="headerlink" href="#moose.seed" title="Permalink to this definition">¶</a></dt>
-<dd><p>Reseed MOOSE random number generator.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>seed</strong> : int</p>
-<blockquote>
-<div><p>Optional value to use for seeding. If 0, a random seed is
-automatically created using the current system time and other
-information. If not specified, it defaults to 0.</p>
-</div></blockquote>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first last">None</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.rand">
-<tt class="descclassname">moose.</tt><tt class="descname">rand</tt><big>(</big><em>) -> [0</em>, <em>1</em><big>)</big><a class="headerlink" href="#moose.rand" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns :</th><td class="field-body">float in [0, 1) real interval generated by MT19937.</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.wildcardFind">
-<tt class="descclassname">moose.</tt><tt class="descname">wildcardFind</tt><big>(</big><em>expression</em><big>)</big> → tuple of melements.<a class="headerlink" href="#moose.wildcardFind" title="Permalink to this definition">¶</a></dt>
-<dd><p>Find an object by wildcard.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters :</th><td class="field-body"><p class="first"><strong>expression</strong> : str</p>
-<blockquote class="last">
-<div><p>MOOSE allows wildcard expressions of the form:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="p">{</span><span class="n">PATH</span><span class="p">}</span><span class="o">/</span><span class="p">{</span><span class="n">WILDCARD</span><span class="p">}[{</span><span class="n">CONDITION</span><span class="p">}]</span>
-</pre></div>
-</div>
-<p>where {PATH} is valid path in the element tree.
-{WILDCARD} can be <cite>#</cite> or <cite>##</cite>.</p>
-<p><cite>#</cite> causes the search to be restricted to the children of the
-element specified by {PATH}.</p>
-<p><cite>##</cite> makes the search to recursively go through all the descendants
-of the {PATH} element.
-{CONDITION} can be:</p>
-<div class="highlight-python"><pre>TYPE={CLASSNAME} : an element satisfies this condition if it is of
-class {CLASSNAME}.
-ISA={CLASSNAME} : alias for TYPE={CLASSNAME}
-CLASS={CLASSNAME} : alias for TYPE={CLASSNAME}
-FIELD({FIELDNAME}){OPERATOR}{VALUE} : compare field {FIELDNAME} with
-{VALUE} by {OPERATOR} where {OPERATOR} is a comparison operator (=,
-!=, >, <, >=, <=).</pre>
-</div>
-<p>For example, /mymodel/##[FIELD(Vm)>=-65] will return a list of all
-the objects under /mymodel whose Vm field is >= -65.</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="moose.quit">
-<tt class="descclassname">moose.</tt><tt class="descname">quit</tt><big>(</big><big>)</big><a class="headerlink" href="#moose.quit" title="Permalink to this definition">¶</a></dt>
-<dd><p>Finalize MOOSE threads and quit MOOSE. This is made available for debugging purpose only. It will automatically get called when moose module is unloaded. End user should not use this function.</p>
-</dd></dl>
-
-</div>
-</div>
-<p>,</p>
-</div>
-
-
- </div>
- </div>
- </div>
- <div class="sphinxsidebar">
- <div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">MOOSE builtins</a><ul>
-<li><a class="reference internal" href="#moose-multiscale-object-oriented-simulation-environment">MOOSE = Multiscale Object Oriented Simulation Environment.</a><ul>
-<li><a class="reference internal" href="#how-to-use-the-documentation">How to use the documentation</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#brief-overview-of-pymoose">Brief overview of PyMOOSE</a><ul>
-<li><a class="reference internal" href="#vec">vec</a></li>
-<li><a class="reference internal" href="#melement">melement</a></li>
-<li><a class="reference internal" href="#creating-melements">Creating melements</a></li>
-<li><a class="reference internal" href="#module-functions">module functions</a></li>
-</ul>
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- <p class="topless"><a href="index.html"
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- title="next chapter">MOOSE Classes</a></p>
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diff --git a/moose-core/Docs/user/html/pymoose/moose_classes.html b/moose-core/Docs/user/html/pymoose/moose_classes.html
deleted file mode 100644
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--- a/moose-core/Docs/user/html/pymoose/moose_classes.html
+++ /dev/null
@@ -1,11794 +0,0 @@
-
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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- accesskey="I">index</a></li>
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- accesskey="P">previous</a> |</li>
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- <div class="document">
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- <div class="bodywrapper">
- <div class="body">
-
- <div class="section" id="moose-classes">
-<h1>MOOSE Classes<a class="headerlink" href="#moose-classes" title="Permalink to this headline">¶</a></h1>
-<dl class="class">
-<dt id="Adaptor">
-<em class="property">class </em><tt class="descname">Adaptor</tt><a class="headerlink" href="#Adaptor" title="Permalink to this definition">¶</a></dt>
-<dd><p>Averages and rescales values to couple different kinds of simulation</p>
-<dl class="attribute">
-<dt id="Adaptor.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Adaptor.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from the scheduler.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.setInputOffset">
-<tt class="descname">setInputOffset</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.setInputOffset" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.getInputOffset">
-<tt class="descname">getInputOffset</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.getInputOffset" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.setOutputOffset">
-<tt class="descname">setOutputOffset</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.setOutputOffset" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.getOutputOffset">
-<tt class="descname">getOutputOffset</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.getOutputOffset" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.setScale">
-<tt class="descname">setScale</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.setScale" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.getScale">
-<tt class="descname">getScale</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.getScale" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.getOutputValue">
-<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.getOutputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.input">
-<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.input" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Input message to the adaptor. If multiple inputs are received, the system averages the inputs.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘process’ call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Adaptor.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Adaptor.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Adaptor.output">
-<tt class="descname">output</tt><a class="headerlink" href="#Adaptor.output" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends the output value every timestep.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Adaptor.requestInput">
-<tt class="descname">requestInput</tt><a class="headerlink" href="#Adaptor.requestInput" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>source message field</em>) Sends out the request. Issued from the process call.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Adaptor.requestField">
-<tt class="descname">requestField</tt><a class="headerlink" href="#Adaptor.requestField" title="Permalink to this definition">¶</a></dt>
-<dd><p>Pd (<em>source message field</em>) Sends out a request to a generic double field. Issued from the process call.Works for any number of targets.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Adaptor.inputOffset">
-<tt class="descname">inputOffset</tt><a class="headerlink" href="#Adaptor.inputOffset" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Offset to apply to input message, before scaling</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Adaptor.outputOffset">
-<tt class="descname">outputOffset</tt><a class="headerlink" href="#Adaptor.outputOffset" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Offset to apply at output, after scaling</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Adaptor.scale">
-<tt class="descname">scale</tt><a class="headerlink" href="#Adaptor.scale" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Scaling factor to apply to input</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Adaptor.outputValue">
-<tt class="descname">outputValue</tt><a class="headerlink" href="#Adaptor.outputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) This is the linearly transformed output.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Annotator">
-<em class="property">class </em><tt class="descname">Annotator</tt><a class="headerlink" href="#Annotator" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="Annotator.setX">
-<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.getX">
-<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.setY">
-<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.getY">
-<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.setZ">
-<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.getZ">
-<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.setNotes">
-<tt class="descname">setNotes</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setNotes" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.getNotes">
-<tt class="descname">getNotes</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getNotes" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.setColor">
-<tt class="descname">setColor</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setColor" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.getColor">
-<tt class="descname">getColor</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getColor" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.setTextColor">
-<tt class="descname">setTextColor</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setTextColor" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.getTextColor">
-<tt class="descname">getTextColor</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getTextColor" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.setIcon">
-<tt class="descname">setIcon</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.setIcon" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Annotator.getIcon">
-<tt class="descname">getIcon</tt><big>(</big><big>)</big><a class="headerlink" href="#Annotator.getIcon" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Annotator.x">
-<tt class="descname">x</tt><a class="headerlink" href="#Annotator.x" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) x field. Typically display coordinate x</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Annotator.y">
-<tt class="descname">y</tt><a class="headerlink" href="#Annotator.y" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) y field. Typically display coordinate y</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Annotator.z">
-<tt class="descname">z</tt><a class="headerlink" href="#Annotator.z" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) z field. Typically display coordinate z</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Annotator.notes">
-<tt class="descname">notes</tt><a class="headerlink" href="#Annotator.notes" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) A string to hold some text notes about parent object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Annotator.color">
-<tt class="descname">color</tt><a class="headerlink" href="#Annotator.color" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) A string to hold a text string specifying display color.Can be a regular English color name, or an rgb code rrrgggbbb</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Annotator.textColor">
-<tt class="descname">textColor</tt><a class="headerlink" href="#Annotator.textColor" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) A string to hold a text string specifying color for text labelthat might be on the display for this object.Can be a regular English color name, or an rgb code rrrgggbbb</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Annotator.icon">
-<tt class="descname">icon</tt><a class="headerlink" href="#Annotator.icon" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) A string to specify icon to use for display</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Arith">
-<em class="property">class </em><tt class="descname">Arith</tt><a class="headerlink" href="#Arith" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="Arith.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Arith.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.setFunction">
-<tt class="descname">setFunction</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.setFunction" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.getFunction">
-<tt class="descname">getFunction</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.getFunction" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.setOutputValue">
-<tt class="descname">setOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.setOutputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.getOutputValue">
-<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.getOutputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.getArg1Value">
-<tt class="descname">getArg1Value</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.getArg1Value" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.setAnyValue">
-<tt class="descname">setAnyValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.setAnyValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.getAnyValue">
-<tt class="descname">getAnyValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.getAnyValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.arg1">
-<tt class="descname">arg1</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.arg1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles argument 1. This just assigns it</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.arg2">
-<tt class="descname">arg2</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.arg2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles argument 2. This just assigns it</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.arg3">
-<tt class="descname">arg3</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.arg3" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles argument 3. This sums in each input, and clears each clock tick.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.arg1x2">
-<tt class="descname">arg1x2</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.arg1x2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Store the product of the two arguments in <a href="#id13"><span class="problematic" id="id14">output_</span></a></p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Arith.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Arith.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Arith.output">
-<tt class="descname">output</tt><a class="headerlink" href="#Arith.output" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out the computed value</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Arith.function">
-<tt class="descname">function</tt><a class="headerlink" href="#Arith.function" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Arithmetic function to perform on inputs.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Arith.outputValue">
-<tt class="descname">outputValue</tt><a class="headerlink" href="#Arith.outputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Value of output as computed last timestep.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Arith.arg1Value">
-<tt class="descname">arg1Value</tt><a class="headerlink" href="#Arith.arg1Value" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Value of arg1 as computed last timestep.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Arith.anyValue">
-<tt class="descname">anyValue</tt><a class="headerlink" href="#Arith.anyValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Value of any of the internal fields, output, arg1, arg2, arg3,as specified by the index argument from 0 to 3.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="BufPool">
-<em class="property">class </em><tt class="descname">BufPool</tt><a class="headerlink" href="#BufPool" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="BufPool.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#BufPool.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="BufPool.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#BufPool.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="BufPool.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#BufPool.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="CaConc">
-<em class="property">class </em><tt class="descname">CaConc</tt><a class="headerlink" href="#CaConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>CaConc: Calcium concentration pool. Takes current from a channel and keeps track of calcium buildup and depletion by a single exponential process.</p>
-<dl class="attribute">
-<dt id="CaConc.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#CaConc.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.setCa">
-<tt class="descname">setCa</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setCa" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.getCa">
-<tt class="descname">getCa</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getCa" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.setCaBasal">
-<tt class="descname">setCaBasal</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setCaBasal" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.getCaBasal">
-<tt class="descname">getCaBasal</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getCaBasal" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.setCa_base">
-<tt class="descname">setCa_base</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setCa_base" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.getCa_base">
-<tt class="descname">getCa_base</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getCa_base" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.setTau">
-<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.getTau">
-<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.setB">
-<tt class="descname">setB</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.getB">
-<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.setThick">
-<tt class="descname">setThick</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setThick" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.getThick">
-<tt class="descname">getThick</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getThick" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.setCeiling">
-<tt class="descname">setCeiling</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setCeiling" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.getCeiling">
-<tt class="descname">getCeiling</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getCeiling" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.setFloor">
-<tt class="descname">setFloor</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.setFloor" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.getFloor">
-<tt class="descname">getFloor</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.getFloor" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.current">
-<tt class="descname">current</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.current" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Calcium Ion current, due to be converted to conc.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.currentFraction">
-<tt class="descname">currentFraction</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.currentFraction" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Fraction of total Ion current, that is carried by Ca2+.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.increase">
-<tt class="descname">increase</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.increase" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Any input current that increases the concentration.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.decrease">
-<tt class="descname">decrease</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.decrease" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Any input current that decreases the concentration.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CaConc.basal">
-<tt class="descname">basal</tt><big>(</big><big>)</big><a class="headerlink" href="#CaConc.basal" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Synonym for assignment of basal conc.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CaConc.concOut">
-<tt class="descname">concOut</tt><a class="headerlink" href="#CaConc.concOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Concentration of Ca in pool</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CaConc.Ca">
-<tt class="descname">Ca</tt><a class="headerlink" href="#CaConc.Ca" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Calcium concentration.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CaConc.CaBasal">
-<tt class="descname">CaBasal</tt><a class="headerlink" href="#CaConc.CaBasal" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Basal Calcium concentration.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CaConc.Ca_base">
-<tt class="descname">Ca_base</tt><a class="headerlink" href="#CaConc.Ca_base" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Basal Calcium concentration, synonym for CaBasal</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CaConc.tau">
-<tt class="descname">tau</tt><a class="headerlink" href="#CaConc.tau" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Settling time for Ca concentration</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CaConc.B">
-<tt class="descname">B</tt><a class="headerlink" href="#CaConc.B" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Volume scaling factor</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CaConc.thick">
-<tt class="descname">thick</tt><a class="headerlink" href="#CaConc.thick" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Thickness of Ca shell.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CaConc.ceiling">
-<tt class="descname">ceiling</tt><a class="headerlink" href="#CaConc.ceiling" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CaConc.floor">
-<tt class="descname">floor</tt><a class="headerlink" href="#CaConc.floor" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Floor value for Ca concentration. If Ca < floor, Ca = floor</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="ChanBase">
-<em class="property">class </em><tt class="descname">ChanBase</tt><a class="headerlink" href="#ChanBase" title="Permalink to this definition">¶</a></dt>
-<dd><p>ChanBase: Base class for assorted ion channels.Presents a common interface for all of them.</p>
-<dl class="attribute">
-<dt id="ChanBase.channel">
-<tt class="descname">channel</tt><a class="headerlink" href="#ChanBase.channel" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChanBase.ghk">
-<tt class="descname">ghk</tt><a class="headerlink" href="#ChanBase.ghk" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Message to Goldman-Hodgkin-Katz object</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChanBase.Vm">
-<tt class="descname">Vm</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.Vm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">Vm</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChanBase.setGbar">
-<tt class="descname">setGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.setGbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChanBase.getGbar">
-<tt class="descname">getGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.getGbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChanBase.setEk">
-<tt class="descname">setEk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.setEk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChanBase.getEk">
-<tt class="descname">getEk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.getEk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChanBase.setGk">
-<tt class="descname">setGk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.setGk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChanBase.getGk">
-<tt class="descname">getGk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.getGk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChanBase.getIk">
-<tt class="descname">getIk</tt><big>(</big><big>)</big><a class="headerlink" href="#ChanBase.getIk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChanBase.channelOut">
-<tt class="descname">channelOut</tt><a class="headerlink" href="#ChanBase.channelOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends channel variables Gk and Ek to compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChanBase.permeabilityOut">
-<tt class="descname">permeabilityOut</tt><a class="headerlink" href="#ChanBase.permeabilityOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Conductance term going out to GHK object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChanBase.IkOut">
-<tt class="descname">IkOut</tt><a class="headerlink" href="#ChanBase.IkOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Channel current. This message typically goes to concenobjects that keep track of ion concentration.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChanBase.Gbar">
-<tt class="descname">Gbar</tt><a class="headerlink" href="#ChanBase.Gbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximal channel conductance</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChanBase.Ek">
-<tt class="descname">Ek</tt><a class="headerlink" href="#ChanBase.Ek" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Reversal potential of channel</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChanBase.Gk">
-<tt class="descname">Gk</tt><a class="headerlink" href="#ChanBase.Gk" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Channel conductance variable</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChanBase.Ik">
-<tt class="descname">Ik</tt><a class="headerlink" href="#ChanBase.Ik" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Channel current variable</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="ChemCompt">
-<em class="property">class </em><tt class="descname">ChemCompt</tt><a class="headerlink" href="#ChemCompt" title="Permalink to this definition">¶</a></dt>
-<dd><p>Pure virtual base class for chemical compartments</p>
-<dl class="method">
-<dt id="ChemCompt.setVolume">
-<tt class="descname">setVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.setVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.getVolume">
-<tt class="descname">getVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.getVoxelVolume">
-<tt class="descname">getVoxelVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getVoxelVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.getOneVoxelVolume">
-<tt class="descname">getOneVoxelVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getOneVoxelVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.getNumDimensions">
-<tt class="descname">getNumDimensions</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getNumDimensions" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.getStencilRate">
-<tt class="descname">getStencilRate</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getStencilRate" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.getStencilIndex">
-<tt class="descname">getStencilIndex</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getStencilIndex" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.buildDefaultMesh">
-<tt class="descname">buildDefaultMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.buildDefaultMesh" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Tells ChemCompt derived class to build a default mesh with thespecified volume and number of meshEntries.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.setVolumeNotRates">
-<tt class="descname">setVolumeNotRates</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.setVolumeNotRates" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Changes volume but does not notify any child objects.Only works if the ChemCompt has just one voxel.This function will invalidate any concentration term inthe model. If you don’t know why you would want to do this,then you shouldn’t use this function.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.resetStencil">
-<tt class="descname">resetStencil</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.resetStencil" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Resets the diffusion stencil to the core stencil that only includes the within-mesh diffusion. This is needed prior to building up the cross-mesh diffusion through junctions.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.setNumMesh">
-<tt class="descname">setNumMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.setNumMesh" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ChemCompt.getNumMesh">
-<tt class="descname">getNumMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#ChemCompt.getNumMesh" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChemCompt.volume">
-<tt class="descname">volume</tt><a class="headerlink" href="#ChemCompt.volume" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Volume of entire chemical domain.Assigning this only works if the chemical compartment hasonly a single voxel. Otherwise ignored.This function goes through all objects below this on thetree, and rescales their molecule #s and rates as per thevolume change. This keeps concentration the same, and alsomaintains rates as expressed in volume units.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChemCompt.voxelVolume">
-<tt class="descname">voxelVolume</tt><a class="headerlink" href="#ChemCompt.voxelVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Vector of volumes of each of the voxels.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChemCompt.numDimensions">
-<tt class="descname">numDimensions</tt><a class="headerlink" href="#ChemCompt.numDimensions" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of spatial dimensions of this compartment. Usually 3 or 2</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChemCompt.oneVoxelVolume">
-<tt class="descname">oneVoxelVolume</tt><a class="headerlink" href="#ChemCompt.oneVoxelVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Volume of specified voxel.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChemCompt.stencilRate">
-<tt class="descname">stencilRate</tt><a class="headerlink" href="#ChemCompt.stencilRate" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,vector<double> (<em>lookup field</em>) vector of diffusion rates in the stencil for specified voxel.The identity of the coupled voxels is given by the partner field ‘stencilIndex’.Returns an empty vector for non-voxelized compartments.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ChemCompt.stencilIndex">
-<tt class="descname">stencilIndex</tt><a class="headerlink" href="#ChemCompt.stencilIndex" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,vector<unsigned int> (<em>lookup field</em>) vector of voxels diffusively coupled to the specified voxel.The diffusion rates into the coupled voxels is given by the partner field ‘stencilRate’.Returns an empty vector for non-voxelized compartments.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Cinfo">
-<em class="property">class </em><tt class="descname">Cinfo</tt><a class="headerlink" href="#Cinfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Class information object.</p>
-<dl class="method">
-<dt id="Cinfo.getDocs">
-<tt class="descname">getDocs</tt><big>(</big><big>)</big><a class="headerlink" href="#Cinfo.getDocs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Cinfo.getBaseClass">
-<tt class="descname">getBaseClass</tt><big>(</big><big>)</big><a class="headerlink" href="#Cinfo.getBaseClass" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Cinfo.docs">
-<tt class="descname">docs</tt><a class="headerlink" href="#Cinfo.docs" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Documentation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Cinfo.baseClass">
-<tt class="descname">baseClass</tt><a class="headerlink" href="#Cinfo.baseClass" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Name of base class</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Clock">
-<em class="property">class </em><tt class="descname">Clock</tt><a class="headerlink" href="#Clock" title="Permalink to this definition">¶</a></dt>
-<dd><p>Clock: Clock class. Handles sequencing of operations in simulations.Every object scheduled for operations in MOOSE is connected to oneof the ‘Tick’ entries on the Clock.The Clock manages ten ‘Ticks’, each of which has its own dt,which is an integral multiple of the base clock <a href="#id15"><span class="problematic" id="id16">dt_</span></a>. On every clock step the ticks are examined to see which of themis due for updating. When a tick is updated, the ‘process’ call of all the objects scheduled on that tick is called.The default scheduling (should not be overridden) has the following assignment of classes to Ticks:0. Biophysics: Init call on Compartments in EE method1. Biophysics: Channels2. Biophysics: Process call on Compartments3. Undefined 4. Kinetics: Pools, or in ksolve mode: Mesh to handle diffusion5. Kinetics: Reacs, enzymes, etc, or in ksolve mode: Stoich/GSL6. Stimulus tables7. More stimulus tables8. Plots9. Postmaster. This must be called last of all and nothing else should use this Tick. The Postmaster is automatically scheduled at set up time. The Tick should be given the longest possible value, typically but not always equal to one of the other ticks, so as to batch the communications. For spiking-only communications, it is usually possible to space the communication tick by as much as 1-2 ms which is the axonal + synaptic delay.</p>
-<dl class="attribute">
-<dt id="Clock.clockControl">
-<tt class="descname">clockControl</tt><a class="headerlink" href="#Clock.clockControl" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Controls all scheduling aspects of Clock, usually from Shell</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc0">
-<tt class="descname">proc0</tt><a class="headerlink" href="#Clock.proc0" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc1">
-<tt class="descname">proc1</tt><a class="headerlink" href="#Clock.proc1" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc2">
-<tt class="descname">proc2</tt><a class="headerlink" href="#Clock.proc2" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc3">
-<tt class="descname">proc3</tt><a class="headerlink" href="#Clock.proc3" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc4">
-<tt class="descname">proc4</tt><a class="headerlink" href="#Clock.proc4" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc5">
-<tt class="descname">proc5</tt><a class="headerlink" href="#Clock.proc5" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc6">
-<tt class="descname">proc6</tt><a class="headerlink" href="#Clock.proc6" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc7">
-<tt class="descname">proc7</tt><a class="headerlink" href="#Clock.proc7" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc8">
-<tt class="descname">proc8</tt><a class="headerlink" href="#Clock.proc8" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.proc9">
-<tt class="descname">proc9</tt><a class="headerlink" href="#Clock.proc9" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared proc/reinit message</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.setDt">
-<tt class="descname">setDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.setDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getDt">
-<tt class="descname">getDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getRunTime">
-<tt class="descname">getRunTime</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getRunTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getCurrentTime">
-<tt class="descname">getCurrentTime</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getCurrentTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getNsteps">
-<tt class="descname">getNsteps</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getNsteps" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getNumTicks">
-<tt class="descname">getNumTicks</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getNumTicks" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getCurrentStep">
-<tt class="descname">getCurrentStep</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getCurrentStep" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getDts">
-<tt class="descname">getDts</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getDts" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getIsRunning">
-<tt class="descname">getIsRunning</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getIsRunning" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.setTickStep">
-<tt class="descname">setTickStep</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.setTickStep" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getTickStep">
-<tt class="descname">getTickStep</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getTickStep" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.setTickDt">
-<tt class="descname">setTickDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.setTickDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.getTickDt">
-<tt class="descname">getTickDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.getTickDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.start">
-<tt class="descname">start</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.start" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Sets off the simulation for the specified duration</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.step">
-<tt class="descname">step</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.step" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Sets off the simulation for the specified # of steps</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.stop">
-<tt class="descname">stop</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.stop" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Halts the simulation, with option to restart seamlessly</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Clock.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Clock.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Zeroes out all ticks, starts at t = 0</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.finished">
-<tt class="descname">finished</tt><a class="headerlink" href="#Clock.finished" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>source message field</em>) Signal for completion of run</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process0">
-<tt class="descname">process0</tt><a class="headerlink" href="#Clock.process0" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 0</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit0">
-<tt class="descname">reinit0</tt><a class="headerlink" href="#Clock.reinit0" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 0</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process1">
-<tt class="descname">process1</tt><a class="headerlink" href="#Clock.process1" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 1</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit1">
-<tt class="descname">reinit1</tt><a class="headerlink" href="#Clock.reinit1" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 1</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process2">
-<tt class="descname">process2</tt><a class="headerlink" href="#Clock.process2" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 2</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit2">
-<tt class="descname">reinit2</tt><a class="headerlink" href="#Clock.reinit2" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 2</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process3">
-<tt class="descname">process3</tt><a class="headerlink" href="#Clock.process3" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 3</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit3">
-<tt class="descname">reinit3</tt><a class="headerlink" href="#Clock.reinit3" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 3</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process4">
-<tt class="descname">process4</tt><a class="headerlink" href="#Clock.process4" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 4</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit4">
-<tt class="descname">reinit4</tt><a class="headerlink" href="#Clock.reinit4" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 4</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process5">
-<tt class="descname">process5</tt><a class="headerlink" href="#Clock.process5" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 5</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit5">
-<tt class="descname">reinit5</tt><a class="headerlink" href="#Clock.reinit5" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 5</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process6">
-<tt class="descname">process6</tt><a class="headerlink" href="#Clock.process6" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 6</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit6">
-<tt class="descname">reinit6</tt><a class="headerlink" href="#Clock.reinit6" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 6</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process7">
-<tt class="descname">process7</tt><a class="headerlink" href="#Clock.process7" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 7</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit7">
-<tt class="descname">reinit7</tt><a class="headerlink" href="#Clock.reinit7" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 7</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process8">
-<tt class="descname">process8</tt><a class="headerlink" href="#Clock.process8" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 8</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit8">
-<tt class="descname">reinit8</tt><a class="headerlink" href="#Clock.reinit8" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 8</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.process9">
-<tt class="descname">process9</tt><a class="headerlink" href="#Clock.process9" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Process for Tick 9</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.reinit9">
-<tt class="descname">reinit9</tt><a class="headerlink" href="#Clock.reinit9" title="Permalink to this definition">¶</a></dt>
-<dd><p>PK8ProcInfo (<em>source message field</em>) Reinit for Tick 9</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#Clock.dt" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Base timestep for simulation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.runTime">
-<tt class="descname">runTime</tt><a class="headerlink" href="#Clock.runTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Duration to run the simulation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.currentTime">
-<tt class="descname">currentTime</tt><a class="headerlink" href="#Clock.currentTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Current simulation time</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.nsteps">
-<tt class="descname">nsteps</tt><a class="headerlink" href="#Clock.nsteps" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of steps to advance the simulation, in units of the smallest timestep on the clock ticks</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.numTicks">
-<tt class="descname">numTicks</tt><a class="headerlink" href="#Clock.numTicks" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of clock ticks</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.currentStep">
-<tt class="descname">currentStep</tt><a class="headerlink" href="#Clock.currentStep" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Current simulation step</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.dts">
-<tt class="descname">dts</tt><a class="headerlink" href="#Clock.dts" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Utility function returning the dt (timestep) of all ticks.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.isRunning">
-<tt class="descname">isRunning</tt><a class="headerlink" href="#Clock.isRunning" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Utility function to report if simulation is in progress.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.tickStep">
-<tt class="descname">tickStep</tt><a class="headerlink" href="#Clock.tickStep" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,unsigned int (<em>lookup field</em>) Step size of specified Tick, as integral multiple of <a href="#id17"><span class="problematic" id="id18">dt_</span></a> A zero step size means that the Tick is inactive</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Clock.tickDt">
-<tt class="descname">tickDt</tt><a class="headerlink" href="#Clock.tickDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Timestep dt of specified Tick. Always integral multiple of <a href="#id19"><span class="problematic" id="id20">dt_</span></a>. If you assign a non-integer multiple it will round off. A zero timestep means that the Tick is inactive</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Compartment">
-<em class="property">class </em><tt class="descname">Compartment</tt><a class="headerlink" href="#Compartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>Compartment object, for branching neuron models.</p>
-</dd></dl>
-
-<dl class="class">
-<dt id="CompartmentBase">
-<em class="property">class </em><tt class="descname">CompartmentBase</tt><a class="headerlink" href="#CompartmentBase" title="Permalink to this definition">¶</a></dt>
-<dd><p>CompartmentBase object, for branching neuron models.</p>
-<dl class="attribute">
-<dt id="CompartmentBase.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#CompartmentBase.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects. The Process should be called _second_ in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.init">
-<tt class="descname">init</tt><a class="headerlink" href="#CompartmentBase.init" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn’t really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.channel">
-<tt class="descname">channel</tt><a class="headerlink" href="#CompartmentBase.channel" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.axial">
-<tt class="descname">axial</tt><a class="headerlink" href="#CompartmentBase.axial" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.raxial">
-<tt class="descname">raxial</tt><a class="headerlink" href="#CompartmentBase.raxial" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setVm">
-<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getVm">
-<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setCm">
-<tt class="descname">setCm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setCm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getCm">
-<tt class="descname">getCm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getCm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setEm">
-<tt class="descname">setEm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setEm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getEm">
-<tt class="descname">getEm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getEm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getIm">
-<tt class="descname">getIm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getIm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setInject">
-<tt class="descname">setInject</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setInject" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getInject">
-<tt class="descname">getInject</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getInject" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setInitVm">
-<tt class="descname">setInitVm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setInitVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getInitVm">
-<tt class="descname">getInitVm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getInitVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setRm">
-<tt class="descname">setRm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setRm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getRm">
-<tt class="descname">getRm</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getRm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setRa">
-<tt class="descname">setRa</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setRa" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getRa">
-<tt class="descname">getRa</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getRa" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setDiameter">
-<tt class="descname">setDiameter</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setDiameter" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getDiameter">
-<tt class="descname">getDiameter</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getDiameter" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setLength">
-<tt class="descname">setLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getLength">
-<tt class="descname">getLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setX0">
-<tt class="descname">setX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setX0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getX0">
-<tt class="descname">getX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getX0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setY0">
-<tt class="descname">setY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setY0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getY0">
-<tt class="descname">getY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getY0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setZ0">
-<tt class="descname">setZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setZ0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getZ0">
-<tt class="descname">getZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getZ0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setX">
-<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getX">
-<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setY">
-<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getY">
-<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.setZ">
-<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.setZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.getZ">
-<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.getZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.injectMsg">
-<tt class="descname">injectMsg</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.injectMsg" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the ‘inject’ field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.randInject">
-<tt class="descname">randInject</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.randInject" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">injectMsg</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the ‘inject’ field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.cable">
-<tt class="descname">cable</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.cable" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Message for organizing compartments into groups, calledcables. Doesn’t do anything.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘process’ call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.initProc">
-<tt class="descname">initProc</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.initProc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles Process call for the ‘init’ phase of the CompartmentBase calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.initReinit">
-<tt class="descname">initReinit</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.initReinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles Reinit call for the ‘init’ phase of the CompartmentBase calculations.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.handleChannel">
-<tt class="descname">handleChannel</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.handleChannel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles conductance and Reversal potential arguments from Channel</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.handleRaxial">
-<tt class="descname">handleRaxial</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.handleRaxial" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles Raxial info: arguments are Ra and Vm.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CompartmentBase.handleAxial">
-<tt class="descname">handleAxial</tt><big>(</big><big>)</big><a class="headerlink" href="#CompartmentBase.handleAxial" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles Axial information. Argument is just Vm.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.VmOut">
-<tt class="descname">VmOut</tt><a class="headerlink" href="#CompartmentBase.VmOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out Vm value of compartment on each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.axialOut">
-<tt class="descname">axialOut</tt><a class="headerlink" href="#CompartmentBase.axialOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out Vm value of compartment to adjacent compartments,on each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.raxialOut">
-<tt class="descname">raxialOut</tt><a class="headerlink" href="#CompartmentBase.raxialOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out Raxial information on each timestep, fields are Ra and Vm</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.Vm">
-<tt class="descname">Vm</tt><a class="headerlink" href="#CompartmentBase.Vm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) membrane potential</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.Cm">
-<tt class="descname">Cm</tt><a class="headerlink" href="#CompartmentBase.Cm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Membrane capacitance</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.Em">
-<tt class="descname">Em</tt><a class="headerlink" href="#CompartmentBase.Em" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Resting membrane potential</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.Im">
-<tt class="descname">Im</tt><a class="headerlink" href="#CompartmentBase.Im" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Current going through membrane</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.inject">
-<tt class="descname">inject</tt><a class="headerlink" href="#CompartmentBase.inject" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Current injection to deliver into compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.initVm">
-<tt class="descname">initVm</tt><a class="headerlink" href="#CompartmentBase.initVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Initial value for membrane potential</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.Rm">
-<tt class="descname">Rm</tt><a class="headerlink" href="#CompartmentBase.Rm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Membrane resistance</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.Ra">
-<tt class="descname">Ra</tt><a class="headerlink" href="#CompartmentBase.Ra" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Axial resistance of compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.diameter">
-<tt class="descname">diameter</tt><a class="headerlink" href="#CompartmentBase.diameter" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Diameter of compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.length">
-<tt class="descname">length</tt><a class="headerlink" href="#CompartmentBase.length" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Length of compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.x0">
-<tt class="descname">x0</tt><a class="headerlink" href="#CompartmentBase.x0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) X coordinate of start of compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.y0">
-<tt class="descname">y0</tt><a class="headerlink" href="#CompartmentBase.y0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Y coordinate of start of compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.z0">
-<tt class="descname">z0</tt><a class="headerlink" href="#CompartmentBase.z0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Z coordinate of start of compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.x">
-<tt class="descname">x</tt><a class="headerlink" href="#CompartmentBase.x" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) x coordinate of end of compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.y">
-<tt class="descname">y</tt><a class="headerlink" href="#CompartmentBase.y" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) y coordinate of end of compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CompartmentBase.z">
-<tt class="descname">z</tt><a class="headerlink" href="#CompartmentBase.z" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) z coordinate of end of compartment</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="CplxEnzBase">
-<em class="property">class </em><tt class="descname">CplxEnzBase</tt><a class="headerlink" href="#CplxEnzBase" title="Permalink to this definition">¶</a></dt>
-<dd><p>: Base class for mass-action enzymes in which there is an explicit pool for the enzyme-substrate complex. It models the reaction: E + S <===> E.S —-> E + P</p>
-<dl class="attribute">
-<dt id="CplxEnzBase.enz">
-<tt class="descname">enz</tt><a class="headerlink" href="#CplxEnzBase.enz" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Connects to enzyme pool</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CplxEnzBase.cplx">
-<tt class="descname">cplx</tt><a class="headerlink" href="#CplxEnzBase.cplx" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Connects to enz-sub complex pool</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.setK1">
-<tt class="descname">setK1</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setK1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.getK1">
-<tt class="descname">getK1</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getK1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.setK2">
-<tt class="descname">setK2</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setK2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.getK2">
-<tt class="descname">getK2</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getK2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.setK3">
-<tt class="descname">setK3</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setK3" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.getK3">
-<tt class="descname">getK3</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getK3" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.setRatio">
-<tt class="descname">setRatio</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setRatio" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.getRatio">
-<tt class="descname">getRatio</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getRatio" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.setConcK1">
-<tt class="descname">setConcK1</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.setConcK1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.getConcK1">
-<tt class="descname">getConcK1</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.getConcK1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.enzDest">
-<tt class="descname">enzDest</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.enzDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles # of molecules of Enzyme</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CplxEnzBase.cplxDest">
-<tt class="descname">cplxDest</tt><big>(</big><big>)</big><a class="headerlink" href="#CplxEnzBase.cplxDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles # of molecules of enz-sub complex</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CplxEnzBase.enzOut">
-<tt class="descname">enzOut</tt><a class="headerlink" href="#CplxEnzBase.enzOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CplxEnzBase.cplxOut">
-<tt class="descname">cplxOut</tt><a class="headerlink" href="#CplxEnzBase.cplxOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CplxEnzBase.k1">
-<tt class="descname">k1</tt><a class="headerlink" href="#CplxEnzBase.k1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Forward reaction from enz + sub to complex, in # units.This parameter is subordinate to the Km. This means thatwhen Km is changed, this changes. It also means that whenk2 or k3 (aka kcat) are changed, we assume that Km remainsfixed, and as a result k1 must change. It is only whenk1 is assigned directly that we assume that the user knowswhat they are doing, and we adjust Km accordingly.k1 is also subordinate to the ‘ratio’ field, since setting the ratio reassigns k2.Should you wish to assign the elementary rates k1, k2, k3,of an enzyme directly, always assign k1 last.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CplxEnzBase.k2">
-<tt class="descname">k2</tt><a class="headerlink" href="#CplxEnzBase.k2" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Reverse reaction from complex to enz + sub</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CplxEnzBase.k3">
-<tt class="descname">k3</tt><a class="headerlink" href="#CplxEnzBase.k3" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Forward rate constant from complex to product + enz</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CplxEnzBase.ratio">
-<tt class="descname">ratio</tt><a class="headerlink" href="#CplxEnzBase.ratio" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Ratio of k2/k3</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CplxEnzBase.concK1">
-<tt class="descname">concK1</tt><a class="headerlink" href="#CplxEnzBase.concK1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) K1 expressed in concentration (1/millimolar.sec) unitsThis parameter is subordinate to the Km. This means thatwhen Km is changed, this changes. It also means that whenk2 or k3 (aka kcat) are changed, we assume that Km remainsfixed, and as a result concK1 must change. It is only whenconcK1 is assigned directly that we assume that the user knowswhat they are doing, and we adjust Km accordingly.concK1 is also subordinate to the ‘ratio’ field, sincesetting the ratio reassigns k2.Should you wish to assign the elementary rates concK1, k2, k3,of an enzyme directly, always assign concK1 last.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="CubeMesh">
-<em class="property">class </em><tt class="descname">CubeMesh</tt><a class="headerlink" href="#CubeMesh" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="CubeMesh.setIsToroid">
-<tt class="descname">setIsToroid</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setIsToroid" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getIsToroid">
-<tt class="descname">getIsToroid</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getIsToroid" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setPreserveNumEntries">
-<tt class="descname">setPreserveNumEntries</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setPreserveNumEntries" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getPreserveNumEntries">
-<tt class="descname">getPreserveNumEntries</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getPreserveNumEntries" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setAlwaysDiffuse">
-<tt class="descname">setAlwaysDiffuse</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setAlwaysDiffuse" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getAlwaysDiffuse">
-<tt class="descname">getAlwaysDiffuse</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getAlwaysDiffuse" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setX0">
-<tt class="descname">setX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setX0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getX0">
-<tt class="descname">getX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getX0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setY0">
-<tt class="descname">setY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setY0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getY0">
-<tt class="descname">getY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getY0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setZ0">
-<tt class="descname">setZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setZ0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getZ0">
-<tt class="descname">getZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getZ0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setX1">
-<tt class="descname">setX1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setX1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getX1">
-<tt class="descname">getX1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getX1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setY1">
-<tt class="descname">setY1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setY1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getY1">
-<tt class="descname">getY1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getY1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setZ1">
-<tt class="descname">setZ1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setZ1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getZ1">
-<tt class="descname">getZ1</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getZ1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setDx">
-<tt class="descname">setDx</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setDx" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getDx">
-<tt class="descname">getDx</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getDx" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setDy">
-<tt class="descname">setDy</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setDy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getDy">
-<tt class="descname">getDy</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getDy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setDz">
-<tt class="descname">setDz</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setDz" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getDz">
-<tt class="descname">getDz</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getDz" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setNx">
-<tt class="descname">setNx</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setNx" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getNx">
-<tt class="descname">getNx</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getNx" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setNy">
-<tt class="descname">setNy</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setNy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getNy">
-<tt class="descname">getNy</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getNy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setNz">
-<tt class="descname">setNz</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setNz" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getNz">
-<tt class="descname">getNz</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getNz" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setCoords">
-<tt class="descname">setCoords</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setCoords" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getCoords">
-<tt class="descname">getCoords</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getCoords" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setMeshToSpace">
-<tt class="descname">setMeshToSpace</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setMeshToSpace" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getMeshToSpace">
-<tt class="descname">getMeshToSpace</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getMeshToSpace" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setSpaceToMesh">
-<tt class="descname">setSpaceToMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setSpaceToMesh" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getSpaceToMesh">
-<tt class="descname">getSpaceToMesh</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getSpaceToMesh" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.setSurface">
-<tt class="descname">setSurface</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.setSurface" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CubeMesh.getSurface">
-<tt class="descname">getSurface</tt><big>(</big><big>)</big><a class="headerlink" href="#CubeMesh.getSurface" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.isToroid">
-<tt class="descname">isToroid</tt><a class="headerlink" href="#CubeMesh.isToroid" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Flag. True when the mesh should be toroidal, that is,when going beyond the right face brings us around to theleft-most mesh entry, and so on. If we have nx, ny, nzentries, this rule means that the coordinate (x, ny, z)will map onto (x, 0, z). Similarly,(-1, y, z) -> (nx-1, y, z)Default is false</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.preserveNumEntries">
-<tt class="descname">preserveNumEntries</tt><a class="headerlink" href="#CubeMesh.preserveNumEntries" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Flag. When it is true, the numbers nx, ny, nz remainunchanged when x0, x1, y0, y1, z0, z1 are altered. Thusdx, dy, dz would change instead. When it is false, thendx, dy, dz remain the same and nx, ny, nz are altered.Default is true</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.alwaysDiffuse">
-<tt class="descname">alwaysDiffuse</tt><a class="headerlink" href="#CubeMesh.alwaysDiffuse" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Flag. When it is true, the mesh matches up sequential mesh entries for diffusion and chmestry. This is regardless of spatial location, and is guaranteed to set up at least the home reaction systemDefault is false</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.x0">
-<tt class="descname">x0</tt><a class="headerlink" href="#CubeMesh.x0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) X coord of one end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.y0">
-<tt class="descname">y0</tt><a class="headerlink" href="#CubeMesh.y0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Y coord of one end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.z0">
-<tt class="descname">z0</tt><a class="headerlink" href="#CubeMesh.z0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Z coord of one end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.x1">
-<tt class="descname">x1</tt><a class="headerlink" href="#CubeMesh.x1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) X coord of other end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.y1">
-<tt class="descname">y1</tt><a class="headerlink" href="#CubeMesh.y1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Y coord of other end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.z1">
-<tt class="descname">z1</tt><a class="headerlink" href="#CubeMesh.z1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Z coord of other end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.dx">
-<tt class="descname">dx</tt><a class="headerlink" href="#CubeMesh.dx" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) X size for mesh</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.dy">
-<tt class="descname">dy</tt><a class="headerlink" href="#CubeMesh.dy" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Y size for mesh</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.dz">
-<tt class="descname">dz</tt><a class="headerlink" href="#CubeMesh.dz" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Z size for mesh</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.nx">
-<tt class="descname">nx</tt><a class="headerlink" href="#CubeMesh.nx" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of subdivisions in mesh in X</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.ny">
-<tt class="descname">ny</tt><a class="headerlink" href="#CubeMesh.ny" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of subdivisions in mesh in Y</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.nz">
-<tt class="descname">nz</tt><a class="headerlink" href="#CubeMesh.nz" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of subdivisions in mesh in Z</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.coords">
-<tt class="descname">coords</tt><a class="headerlink" href="#CubeMesh.coords" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Set all the coords of the cuboid at once. Order is:x0 y0 z0 x1 y1 z1 dx dy dzWhen this is done, it recalculates the numEntries since dx, dy and dz are given explicitly.As a special hack, you can leave out dx, dy and dz and use a vector of size 6. In this case the operation assumes that nx, ny and nz are to be preserved and dx, dy and dz will be recalculated.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.meshToSpace">
-<tt class="descname">meshToSpace</tt><a class="headerlink" href="#CubeMesh.meshToSpace" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int> (<em>value field</em>) Array in which each mesh entry stores spatial (cubic) index</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.spaceToMesh">
-<tt class="descname">spaceToMesh</tt><a class="headerlink" href="#CubeMesh.spaceToMesh" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int> (<em>value field</em>) Array in which each space index (obtained by linearizing the xyz coords) specifies which meshIndex is present.In many cases the index will store the EMPTY flag if there isno mesh entry at that spatial location</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CubeMesh.surface">
-<tt class="descname">surface</tt><a class="headerlink" href="#CubeMesh.surface" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int> (<em>value field</em>) Array specifying surface of arbitrary volume within the CubeMesh. All entries must fall within the cuboid. Each entry of the array is a spatial index obtained by linearizing the ix, iy, iz coordinates within the cuboid. So, each entry == ( iz * ny + iy ) * nx + ixNote that the voxels listed on the surface are WITHIN the volume of the CubeMesh object</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="CylMesh">
-<em class="property">class </em><tt class="descname">CylMesh</tt><a class="headerlink" href="#CylMesh" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="CylMesh.setX0">
-<tt class="descname">setX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setX0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getX0">
-<tt class="descname">getX0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getX0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.setY0">
-<tt class="descname">setY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setY0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getY0">
-<tt class="descname">getY0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getY0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.setZ0">
-<tt class="descname">setZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setZ0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getZ0">
-<tt class="descname">getZ0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getZ0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.setR0">
-<tt class="descname">setR0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setR0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getR0">
-<tt class="descname">getR0</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getR0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.setX1">
-<tt class="descname">setX1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setX1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getX1">
-<tt class="descname">getX1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getX1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.setY1">
-<tt class="descname">setY1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setY1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getY1">
-<tt class="descname">getY1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getY1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.setZ1">
-<tt class="descname">setZ1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setZ1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getZ1">
-<tt class="descname">getZ1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getZ1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.setR1">
-<tt class="descname">setR1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setR1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getR1">
-<tt class="descname">getR1</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getR1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.setDiffLength">
-<tt class="descname">setDiffLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setDiffLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getDiffLength">
-<tt class="descname">getDiffLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getDiffLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.setCoords">
-<tt class="descname">setCoords</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.setCoords" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getCoords">
-<tt class="descname">getCoords</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getCoords" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getNumDiffCompts">
-<tt class="descname">getNumDiffCompts</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getNumDiffCompts" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="CylMesh.getTotLength">
-<tt class="descname">getTotLength</tt><big>(</big><big>)</big><a class="headerlink" href="#CylMesh.getTotLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.x0">
-<tt class="descname">x0</tt><a class="headerlink" href="#CylMesh.x0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) x coord of one end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.y0">
-<tt class="descname">y0</tt><a class="headerlink" href="#CylMesh.y0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) y coord of one end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.z0">
-<tt class="descname">z0</tt><a class="headerlink" href="#CylMesh.z0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) z coord of one end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.r0">
-<tt class="descname">r0</tt><a class="headerlink" href="#CylMesh.r0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Radius of one end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.x1">
-<tt class="descname">x1</tt><a class="headerlink" href="#CylMesh.x1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) x coord of other end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.y1">
-<tt class="descname">y1</tt><a class="headerlink" href="#CylMesh.y1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) y coord of other end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.z1">
-<tt class="descname">z1</tt><a class="headerlink" href="#CylMesh.z1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) z coord of other end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.r1">
-<tt class="descname">r1</tt><a class="headerlink" href="#CylMesh.r1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Radius of other end</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.diffLength">
-<tt class="descname">diffLength</tt><a class="headerlink" href="#CylMesh.diffLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Length constant to use for subdivisionsThe system will attempt to subdivide using compartments oflength diffLength on average. If the cylinder has different enddiameters r0 and r1, it will scale to smaller lengthsfor the smaller diameter end and vice versa.Once the value is set it will recompute diffLength as totLength/numEntries</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.coords">
-<tt class="descname">coords</tt><a class="headerlink" href="#CylMesh.coords" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) All the coords as a single vector: x0 y0 z0 x1 y1 z1 r0 r1 diffLength</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.numDiffCompts">
-<tt class="descname">numDiffCompts</tt><a class="headerlink" href="#CylMesh.numDiffCompts" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of diffusive compartments in model</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="CylMesh.totLength">
-<tt class="descname">totLength</tt><a class="headerlink" href="#CylMesh.totLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Total length of cylinder</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="DiagonalMsg">
-<em class="property">class </em><tt class="descname">DiagonalMsg</tt><a class="headerlink" href="#DiagonalMsg" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="DiagonalMsg.setStride">
-<tt class="descname">setStride</tt><big>(</big><big>)</big><a class="headerlink" href="#DiagonalMsg.setStride" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiagonalMsg.getStride">
-<tt class="descname">getStride</tt><big>(</big><big>)</big><a class="headerlink" href="#DiagonalMsg.getStride" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="DiagonalMsg.stride">
-<tt class="descname">stride</tt><a class="headerlink" href="#DiagonalMsg.stride" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) The stride is the increment to the src DataId that gives thedest DataId. It can be positive or negative, but bounds checkingtakes place and it does not wrap around.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="DifShell">
-<em class="property">class </em><tt class="descname">DifShell</tt><a class="headerlink" href="#DifShell" title="Permalink to this definition">¶</a></dt>
-<dd><blockquote>
-<div><p>DifShell object: Models diffusion of an ion (typically calcium) within an electric compartment. A DifShell is an iso-concentration region with respect to the ion. Adjoining DifShells exchange flux of this ion, and also keep track of changes in concentration due to pumping, buffering and channel currents, by talking to the appropriate objects.</p>
-<dl class="attribute">
-<dt id="DifShell.process_0">
-<tt class="descname">process_0</tt><a class="headerlink" href="#DifShell.process_0" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Here we create 2 shared finfos to attach with the Ticks. This is because we want to perform DifShell computations in 2 stages, much as in the Compartment object. In the first stage we send out the concentration value to other DifShells and Buffer elements. We also receive fluxes and currents and sum them up to compute ( dC / dt ). In the second stage we find the new C value using an explicit integration method. This 2-stage procedure eliminates the need to store and send prev_C values, as was common in GENESIS.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="DifShell.process_1">
-<tt class="descname">process_1</tt><a class="headerlink" href="#DifShell.process_1" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Second process call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="DifShell.buffer">
-<tt class="descname">buffer</tt><a class="headerlink" href="#DifShell.buffer" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message from a DifShell to a Buffer (FixBuffer or DifBuffer). During stage 0:</p>
-</dd></dl>
-
-</div></blockquote>
-<ul class="simple">
-<li>DifShell sends ion concentration</li>
-</ul>
-</dd></dl>
-
-<ul class="simple">
-<li>Buffer updates buffer concentration and sends it back immediately using a call-back.</li>
-<li>DifShell updates the time-derivative ( dC / dt )</li>
-</ul>
-<p>During stage 1:
-- DifShell advances concentration C
-This scheme means that the Buffer does not need to be scheduled, and it does its computations when it receives a cue from the DifShell. May not be the best idea, but it saves us from doing the above computations in 3 stages instead of 2.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="innerDif">
-<tt class="descname">innerDif</tt><a class="headerlink" href="#innerDif" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This shared message (and the next) is between DifShells: adjoining shells exchange information to find out the flux between them. Using this message, an inner shell sends to, and receives from its outer shell.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="outerDif">
-<tt class="descname">outerDif</tt><a class="headerlink" href="#outerDif" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Using this message, an outer shell sends to, and receives from its inner shell.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getC">
-<tt class="descname">getC</tt><big>(</big><big>)</big><a class="headerlink" href="#getC" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setCeq">
-<tt class="descname">setCeq</tt><big>(</big><big>)</big><a class="headerlink" href="#setCeq" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getCeq">
-<tt class="descname">getCeq</tt><big>(</big><big>)</big><a class="headerlink" href="#getCeq" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setD">
-<tt class="descname">setD</tt><big>(</big><big>)</big><a class="headerlink" href="#setD" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getD">
-<tt class="descname">getD</tt><big>(</big><big>)</big><a class="headerlink" href="#getD" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setValence">
-<tt class="descname">setValence</tt><big>(</big><big>)</big><a class="headerlink" href="#setValence" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getValence">
-<tt class="descname">getValence</tt><big>(</big><big>)</big><a class="headerlink" href="#getValence" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setLeak">
-<tt class="descname">setLeak</tt><big>(</big><big>)</big><a class="headerlink" href="#setLeak" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getLeak">
-<tt class="descname">getLeak</tt><big>(</big><big>)</big><a class="headerlink" href="#getLeak" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setShapeMode">
-<tt class="descname">setShapeMode</tt><big>(</big><big>)</big><a class="headerlink" href="#setShapeMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getShapeMode">
-<tt class="descname">getShapeMode</tt><big>(</big><big>)</big><a class="headerlink" href="#getShapeMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setLength">
-<tt class="descname">setLength</tt><big>(</big><big>)</big><a class="headerlink" href="#setLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getLength">
-<tt class="descname">getLength</tt><big>(</big><big>)</big><a class="headerlink" href="#getLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setDiameter">
-<tt class="descname">setDiameter</tt><big>(</big><big>)</big><a class="headerlink" href="#setDiameter" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getDiameter">
-<tt class="descname">getDiameter</tt><big>(</big><big>)</big><a class="headerlink" href="#getDiameter" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setThickness">
-<tt class="descname">setThickness</tt><big>(</big><big>)</big><a class="headerlink" href="#setThickness" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getThickness">
-<tt class="descname">getThickness</tt><big>(</big><big>)</big><a class="headerlink" href="#getThickness" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setVolume">
-<tt class="descname">setVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#setVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getVolume">
-<tt class="descname">getVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#getVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setOuterArea">
-<tt class="descname">setOuterArea</tt><big>(</big><big>)</big><a class="headerlink" href="#setOuterArea" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getOuterArea">
-<tt class="descname">getOuterArea</tt><big>(</big><big>)</big><a class="headerlink" href="#getOuterArea" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setInnerArea">
-<tt class="descname">setInnerArea</tt><big>(</big><big>)</big><a class="headerlink" href="#setInnerArea" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getInnerArea">
-<tt class="descname">getInnerArea</tt><big>(</big><big>)</big><a class="headerlink" href="#getInnerArea" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Reinit happens only in stage 0</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">process</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handle process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">reinit</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Reinit happens only in stage 0</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="reaction">
-<tt class="descname">reaction</tt><big>(</big><big>)</big><a class="headerlink" href="#reaction" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Here the DifShell receives reaction rates (forward and backward), and concentrations for the free-buffer and bound-buffer molecules.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="fluxFromOut">
-<tt class="descname">fluxFromOut</tt><big>(</big><big>)</big><a class="headerlink" href="#fluxFromOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Destination message</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="fluxFromIn">
-<tt class="descname">fluxFromIn</tt><big>(</big><big>)</big><a class="headerlink" href="#fluxFromIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="influx">
-<tt class="descname">influx</tt><big>(</big><big>)</big><a class="headerlink" href="#influx" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="outflux">
-<tt class="descname">outflux</tt><big>(</big><big>)</big><a class="headerlink" href="#outflux" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="fInflux">
-<tt class="descname">fInflux</tt><big>(</big><big>)</big><a class="headerlink" href="#fInflux" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="fOutflux">
-<tt class="descname">fOutflux</tt><big>(</big><big>)</big><a class="headerlink" href="#fOutflux" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="storeInflux">
-<tt class="descname">storeInflux</tt><big>(</big><big>)</big><a class="headerlink" href="#storeInflux" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="storeOutflux">
-<tt class="descname">storeOutflux</tt><big>(</big><big>)</big><a class="headerlink" href="#storeOutflux" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="tauPump">
-<tt class="descname">tauPump</tt><big>(</big><big>)</big><a class="headerlink" href="#tauPump" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="eqTauPump">
-<tt class="descname">eqTauPump</tt><big>(</big><big>)</big><a class="headerlink" href="#eqTauPump" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="mmPump">
-<tt class="descname">mmPump</tt><big>(</big><big>)</big><a class="headerlink" href="#mmPump" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="hillPump">
-<tt class="descname">hillPump</tt><big>(</big><big>)</big><a class="headerlink" href="#hillPump" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="concentrationOut">
-<tt class="descname">concentrationOut</tt><a class="headerlink" href="#concentrationOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out concentration</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="innerDifSourceOut">
-<tt class="descname">innerDifSourceOut</tt><a class="headerlink" href="#innerDifSourceOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out source information.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="outerDifSourceOut">
-<tt class="descname">outerDifSourceOut</tt><a class="headerlink" href="#outerDifSourceOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out source information.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="C">
-<tt class="descname">C</tt><a class="headerlink" href="#C" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Concentration C is computed by the DifShell and is read-only</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ceq">
-<tt class="descname">Ceq</tt><a class="headerlink" href="#Ceq" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="D">
-<tt class="descname">D</tt><a class="headerlink" href="#D" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="valence">
-<tt class="descname">valence</tt><a class="headerlink" href="#valence" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="leak">
-<tt class="descname">leak</tt><a class="headerlink" href="#leak" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="shapeMode">
-<tt class="descname">shapeMode</tt><a class="headerlink" href="#shapeMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="length">
-<tt class="descname">length</tt><a class="headerlink" href="#length" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="diameter">
-<tt class="descname">diameter</tt><a class="headerlink" href="#diameter" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="thickness">
-<tt class="descname">thickness</tt><a class="headerlink" href="#thickness" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="volume">
-<tt class="descname">volume</tt><a class="headerlink" href="#volume" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="outerArea">
-<tt class="descname">outerArea</tt><a class="headerlink" href="#outerArea" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="innerArea">
-<tt class="descname">innerArea</tt><a class="headerlink" href="#innerArea" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>)</p>
-</dd></dl>
-
-</div></blockquote>
-<dl class="class">
-<dt id="DiffAmp">
-<em class="property">class </em><tt class="descname">DiffAmp</tt><a class="headerlink" href="#DiffAmp" title="Permalink to this definition">¶</a></dt>
-<dd><p>A difference amplifier. Output is the difference between the total plus inputs and the total minus inputs multiplied by gain. Gain can be set statically as a field or can be a destination message and thus dynamically determined by the output of another object. Same as GENESIS diffamp object.</p>
-<dl class="attribute">
-<dt id="DiffAmp.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#DiffAmp.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.setGain">
-<tt class="descname">setGain</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.setGain" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.getGain">
-<tt class="descname">getGain</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.getGain" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.setSaturation">
-<tt class="descname">setSaturation</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.setSaturation" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.getSaturation">
-<tt class="descname">getSaturation</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.getSaturation" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.getOutputValue">
-<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.getOutputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.gainIn">
-<tt class="descname">gainIn</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.gainIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Destination message to control gain dynamically.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.plusIn">
-<tt class="descname">plusIn</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.plusIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Positive input terminal of the amplifier. All the messages connected here are summed up to get total positive input.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.minusIn">
-<tt class="descname">minusIn</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.minusIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Negative input terminal of the amplifier. All the messages connected here are summed up to get total positive input.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="DiffAmp.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#DiffAmp.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="DiffAmp.output">
-<tt class="descname">output</tt><a class="headerlink" href="#DiffAmp.output" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Current output level.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="DiffAmp.gain">
-<tt class="descname">gain</tt><a class="headerlink" href="#DiffAmp.gain" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Gain of the amplifier. The output of the amplifier is the difference between the totals in plus and minus inputs multiplied by the gain. Defaults to 1</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="DiffAmp.saturation">
-<tt class="descname">saturation</tt><a class="headerlink" href="#DiffAmp.saturation" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Saturation is the bound on the output. If output goes beyond the +/-saturation range, it is truncated to the closer of +saturation and -saturation. Defaults to the maximum double precision floating point number representable on the system.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="DiffAmp.outputValue">
-<tt class="descname">outputValue</tt><a class="headerlink" href="#DiffAmp.outputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Output of the amplifier, i.e. gain * (plus - minus).</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Double">
-<em class="property">class </em><tt class="descname">Double</tt><a class="headerlink" href="#Double" title="Permalink to this definition">¶</a></dt>
-<dd><p>Variable for storing values.</p>
-<dl class="method">
-<dt id="Double.setValue">
-<tt class="descname">setValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Double.setValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Double.getValue">
-<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Double.getValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Double.value">
-<tt class="descname">value</tt><a class="headerlink" href="#Double.value" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Variable value</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Dsolve">
-<em class="property">class </em><tt class="descname">Dsolve</tt><a class="headerlink" href="#Dsolve" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="Dsolve.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Dsolve.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.setStoich">
-<tt class="descname">setStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setStoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.getStoich">
-<tt class="descname">getStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getStoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.setPath">
-<tt class="descname">setPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setPath" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.getPath">
-<tt class="descname">getPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getPath" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.setCompartment">
-<tt class="descname">setCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setCompartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.getCompartment">
-<tt class="descname">getCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getCompartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.getNumVoxels">
-<tt class="descname">getNumVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getNumVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.getNumAllVoxels">
-<tt class="descname">getNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getNumAllVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.setNVec">
-<tt class="descname">setNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setNVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.getNVec">
-<tt class="descname">getNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getNVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.setNumPools">
-<tt class="descname">setNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.setNumPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.getNumPools">
-<tt class="descname">getNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.getNumPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.buildNeuroMeshJunctions">
-<tt class="descname">buildNeuroMeshJunctions</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.buildNeuroMeshJunctions" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Builds junctions between NeuroMesh, SpineMesh and PsdMesh</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Dsolve.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Dsolve.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Dsolve.stoich">
-<tt class="descname">stoich</tt><a class="headerlink" href="#Dsolve.stoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Stoichiometry object for handling this reaction system.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Dsolve.path">
-<tt class="descname">path</tt><a class="headerlink" href="#Dsolve.path" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Path of reaction system. Must include all the pools that are to be handled by the Dsolve, can also include other random objects, which will be ignored.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Dsolve.compartment">
-<tt class="descname">compartment</tt><a class="headerlink" href="#Dsolve.compartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Reac-diff compartment in which this diffusion system is embedded.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Dsolve.numVoxels">
-<tt class="descname">numVoxels</tt><a class="headerlink" href="#Dsolve.numVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of voxels in the core reac-diff system, on the current diffusion solver.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Dsolve.numAllVoxels">
-<tt class="descname">numAllVoxels</tt><a class="headerlink" href="#Dsolve.numAllVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of voxels in the core reac-diff system, on the current diffusion solver.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Dsolve.numPools">
-<tt class="descname">numPools</tt><a class="headerlink" href="#Dsolve.numPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Dsolve.nVec">
-<tt class="descname">nVec</tt><a class="headerlink" href="#Dsolve.nVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,vector<double> (<em>lookup field</em>) vector of # of molecules along diffusion length, looked up by pool index</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Enz">
-<em class="property">class </em><tt class="descname">Enz</tt><a class="headerlink" href="#Enz" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="EnzBase">
-<em class="property">class </em><tt class="descname">EnzBase</tt><a class="headerlink" href="#EnzBase" title="Permalink to this definition">¶</a></dt>
-<dd><p>Abstract base class for enzymes.</p>
-<dl class="attribute">
-<dt id="EnzBase.sub">
-<tt class="descname">sub</tt><a class="headerlink" href="#EnzBase.sub" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Connects to substrate molecule</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="EnzBase.prd">
-<tt class="descname">prd</tt><a class="headerlink" href="#EnzBase.prd" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Connects to product molecule</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="EnzBase.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#EnzBase.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.setKm">
-<tt class="descname">setKm</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.setKm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.getKm">
-<tt class="descname">getKm</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.getKm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.setNumKm">
-<tt class="descname">setNumKm</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.setNumKm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.getNumKm">
-<tt class="descname">getNumKm</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.getNumKm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.setKcat">
-<tt class="descname">setKcat</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.setKcat" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.getKcat">
-<tt class="descname">getKcat</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.getKcat" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.getNumSubstrates">
-<tt class="descname">getNumSubstrates</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.getNumSubstrates" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.enzDest">
-<tt class="descname">enzDest</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.enzDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles # of molecules of Enzyme</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.subDest">
-<tt class="descname">subDest</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.subDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles # of molecules of substrate</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.prdDest">
-<tt class="descname">prdDest</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.prdDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles # of molecules of product. Dummy.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="EnzBase.remesh">
-<tt class="descname">remesh</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzBase.remesh" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Tells the MMEnz to recompute its numKm after remeshing</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="EnzBase.subOut">
-<tt class="descname">subOut</tt><a class="headerlink" href="#EnzBase.subOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="EnzBase.prdOut">
-<tt class="descname">prdOut</tt><a class="headerlink" href="#EnzBase.prdOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="EnzBase.Km">
-<tt class="descname">Km</tt><a class="headerlink" href="#EnzBase.Km" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Michaelis-Menten constant in SI conc units (milliMolar)</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="EnzBase.numKm">
-<tt class="descname">numKm</tt><a class="headerlink" href="#EnzBase.numKm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Michaelis-Menten constant in number units, volume dependent</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="EnzBase.kcat">
-<tt class="descname">kcat</tt><a class="headerlink" href="#EnzBase.kcat" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Forward rate constant for enzyme, units 1/sec</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="EnzBase.numSubstrates">
-<tt class="descname">numSubstrates</tt><a class="headerlink" href="#EnzBase.numSubstrates" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Finfo">
-<em class="property">class </em><tt class="descname">Finfo</tt><a class="headerlink" href="#Finfo" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="Finfo.getFieldName">
-<tt class="descname">getFieldName</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getFieldName" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Finfo.getDocs">
-<tt class="descname">getDocs</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getDocs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Finfo.getType">
-<tt class="descname">getType</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getType" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Finfo.getSrc">
-<tt class="descname">getSrc</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getSrc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Finfo.getDest">
-<tt class="descname">getDest</tt><big>(</big><big>)</big><a class="headerlink" href="#Finfo.getDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Finfo.fieldName">
-<tt class="descname">fieldName</tt><a class="headerlink" href="#Finfo.fieldName" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Name of field handled by Finfo</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Finfo.docs">
-<tt class="descname">docs</tt><a class="headerlink" href="#Finfo.docs" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Documentation for Finfo</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Finfo.type">
-<tt class="descname">type</tt><a class="headerlink" href="#Finfo.type" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) RTTI type info for this Finfo</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Finfo.src">
-<tt class="descname">src</tt><a class="headerlink" href="#Finfo.src" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) Subsidiary SrcFinfos. Useful for SharedFinfos</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Finfo.dest">
-<tt class="descname">dest</tt><a class="headerlink" href="#Finfo.dest" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) Subsidiary DestFinfos. Useful for SharedFinfos</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Func">
-<em class="property">class </em><tt class="descname">Func</tt><a class="headerlink" href="#Func" title="Permalink to this definition">¶</a></dt>
-<dd><p>Func: general purpose function calculator using real numbers. It can</p>
-<p>parse mathematical expression defining a function and evaluate it</p>
-<p>and/or its derivative for specified variable values.</p>
-<p>The variables can be input from other moose objects. In case of</p>
-<p>arbitrary variable names, the source message must have the variable</p>
-<p>name as the first argument. For most common cases, input messages to</p>
-<p>set x, y, z and xy, xyz are made available without such</p>
-<p>requirement. This class handles only real numbers</p>
-<blockquote>
-<div>pi=3.141592...,</div></blockquote>
-<p>e=2.718281...</p>
-<dl class="attribute">
-<dt id="Func.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Func.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.getValue">
-<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.getDerivative">
-<tt class="descname">getDerivative</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getDerivative" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.setMode">
-<tt class="descname">setMode</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.getMode">
-<tt class="descname">getMode</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.setExpr">
-<tt class="descname">setExpr</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setExpr" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.getExpr">
-<tt class="descname">getExpr</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getExpr" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.setVar">
-<tt class="descname">setVar</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setVar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.getVar">
-<tt class="descname">getVar</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getVar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.getVars">
-<tt class="descname">getVars</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getVars" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.setX">
-<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.getX">
-<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.setY">
-<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.getY">
-<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.setZ">
-<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.setZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.getZ">
-<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.getZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.varIn">
-<tt class="descname">varIn</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.varIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle value for specified variable coming from other objects</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Func.xIn">
-<tt class="descname">xIn</tt><big>(</big><big>)</big><a class="headerlink" href="#Func.xIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle value for variable named x. This is a shorthand. If the</p>
-</dd></dl>
-
-</dd></dl>
-
-<p>expression does not have any variable named x, this the first variable
-in the sequence <cite>vars</cite>.</p>
-<blockquote>
-<div><blockquote>
-<div><dl class="method">
-<dt id="yIn">
-<tt class="descname">yIn</tt><big>(</big><big>)</big><a class="headerlink" href="#yIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle value for variable named y. This is a utility for two/three</p>
-</dd></dl>
-
-</div></blockquote>
-<p>variable functions where the y value comes from a source separate
-from that of x. This is a shorthand. If the</p>
-</div></blockquote>
-<p>expression does not have any variable named y, this the second
-variable in the sequence <cite>vars</cite>.</p>
-<blockquote>
-<div><blockquote>
-<div><dl class="method">
-<dt id="zIn">
-<tt class="descname">zIn</tt><big>(</big><big>)</big><a class="headerlink" href="#zIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle value for variable named z. This is a utility for three</p>
-</dd></dl>
-
-</div></blockquote>
-<p>variable functions where the z value comes from a source separate
-from that of x or y. This is a shorthand. If the expression does not
-have any variable named y, this the second variable in the sequence <cite>vars</cite>.</p>
-<blockquote>
-<div><dl class="method">
-<dt id="xyIn">
-<tt class="descname">xyIn</tt><big>(</big><big>)</big><a class="headerlink" href="#xyIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle value for variables x and y for two-variable function</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="xyzIn">
-<tt class="descname">xyzIn</tt><big>(</big><big>)</big><a class="headerlink" href="#xyzIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle value for variables x, y and z for three-variable function</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">process</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">reinit</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="valueOut">
-<tt class="descname">valueOut</tt><a class="headerlink" href="#valueOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Evaluated value of the function for the current variable values.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="derivativeOut">
-<tt class="descname">derivativeOut</tt><a class="headerlink" href="#derivativeOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Value of derivative of the function for the current variable values</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="value">
-<tt class="descname">value</tt><a class="headerlink" href="#value" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Result of the function evaluation with current variable values.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="derivative">
-<tt class="descname">derivative</tt><a class="headerlink" href="#derivative" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Derivative of the function at given variable values.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="mode">
-<tt class="descname">mode</tt><a class="headerlink" href="#mode" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Mode of operation:</p>
-</dd></dl>
-
-</div></blockquote>
-<p>1: only the function value will be funculated
-2: only the derivative will be funculated
-3: both function value and derivative at current variable values will be funculated.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="expr">
-<tt class="descname">expr</tt><a class="headerlink" href="#expr" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Mathematical expression defining the function. The underlying parser</p>
-</dd></dl>
-
-</div></blockquote>
-</div></blockquote>
-<p>is muParser. Hence the available functions and operators are (from
-muParser docs):</p>
-<p>Functions
-Name args explanation
-sin 1 sine function
-cos 1 cosine function
-tan 1 tangens function
-asin 1 arcus sine function
-acos 1 arcus cosine function
-atan 1 arcus tangens function
-sinh 1 hyperbolic sine function
-cosh 1 hyperbolic cosine
-tanh 1 hyperbolic tangens function
-asinh 1 hyperbolic arcus sine function
-acosh 1 hyperbolic arcus tangens function
-atanh 1 hyperbolic arcur tangens function
-log2 1 logarithm to the base 2
-log10 1 logarithm to the base 10
-log 1 logarithm to the base 10
-ln 1 logarithm to base e (2.71828...)
-exp 1 e raised to the power of x
-sqrt 1 square root of a value
-sign 1 sign function -1 if x<0; 1 if x>0
-rint 1 round to nearest integer
-abs 1 absolute value
-min var. min of all arguments
-max var. max of all arguments
-sum var. sum of all arguments
-avg var. mean value of all arguments</p>
-<p>Operators
-Op meaning prioroty
-= assignement -1
-&& logical and 1
-|| logical or 2
-<= less or equal 4
->= greater or equal 4
-!= not equal 4
-== equal 4
-> greater than 4
-< less than 4
-+ addition 5
-- subtraction 5
-* multiplication 6
-/ division 6
-^ raise x to the power of y 7</p>
-<p>?: if then else operator C++ style syntax</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="vars">
-<tt class="descname">vars</tt><a class="headerlink" href="#vars" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) Variable names in the expression</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="x">
-<tt class="descname">x</tt><a class="headerlink" href="#x" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Value for variable named x. This is a shorthand. If the</p>
-</dd></dl>
-
-</div></blockquote>
-<p>expression does not have any variable named x, this the first variable
-in the sequence <cite>vars</cite>.</p>
-<blockquote>
-<div><blockquote>
-<div><dl class="attribute">
-<dt id="y">
-<tt class="descname">y</tt><a class="headerlink" href="#y" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Value for variable named y. This is a utility for two/three</p>
-</dd></dl>
-
-</div></blockquote>
-<p>variable functions where the y value comes from a source separate
-from that of x. This is a shorthand. If the</p>
-</div></blockquote>
-<p>expression does not have any variable named y, this the second
-variable in the sequence <cite>vars</cite>.</p>
-<blockquote>
-<div><blockquote>
-<div><dl class="attribute">
-<dt id="z">
-<tt class="descname">z</tt><a class="headerlink" href="#z" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Value for variable named z. This is a utility for three</p>
-</dd></dl>
-
-</div></blockquote>
-<p>variable functions where the z value comes from a source separate
-from that of x or z. This is a shorthand. If the expression does not
-have any variable named z, this the third variable in the sequence <cite>vars</cite>.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="var">
-<tt class="descname">var</tt><a class="headerlink" href="#var" title="Permalink to this definition">¶</a></dt>
-<dd><p>string,double (<em>lookup field</em>) Lookup table for variable values.</p>
-</dd></dl>
-
-</div></blockquote>
-</div></blockquote>
-<dl class="class">
-<dt id="FuncBase">
-<em class="property">class </em><tt class="descname">FuncBase</tt><a class="headerlink" href="#FuncBase" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="FuncBase.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#FuncBase.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="FuncBase.getResult">
-<tt class="descname">getResult</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncBase.getResult" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="FuncBase.input">
-<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncBase.input" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="FuncBase.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncBase.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="FuncBase.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncBase.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="FuncBase.output">
-<tt class="descname">output</tt><a class="headerlink" href="#FuncBase.output" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out sum on each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="FuncBase.result">
-<tt class="descname">result</tt><a class="headerlink" href="#FuncBase.result" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Outcome of function computation</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="FuncPool">
-<em class="property">class </em><tt class="descname">FuncPool</tt><a class="headerlink" href="#FuncPool" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="FuncPool.input">
-<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#FuncPool.input" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles input to control value of <a href="#id21"><span class="problematic" id="id22">n_</span></a></p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="GapJunction">
-<em class="property">class </em><tt class="descname">GapJunction</tt><a class="headerlink" href="#GapJunction" title="Permalink to this definition">¶</a></dt>
-<dd><p>Implementation of gap junction between two compartments. The shared</p>
-<p>fields, ‘channel1’ and ‘channel2’ can be connected to the ‘channel’</p>
-<p>message of the compartments at either end of the gap junction. The</p>
-<p>compartments will send their Vm to the gap junction and receive the</p>
-<p>conductance ‘Gk’ of the gap junction and the Vm of the other</p>
-<p>compartment.</p>
-<dl class="attribute">
-<dt id="GapJunction.channel1">
-<tt class="descname">channel1</tt><a class="headerlink" href="#GapJunction.channel1" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to couple the conductance and Vm from</p>
-</dd></dl>
-
-</dd></dl>
-
-<p>terminal 2 to the compartment at terminal 1. The first entry is source
-sending out Gk and Vm2, the second entry is destination for Vm1.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="channel2">
-<tt class="descname">channel2</tt><a class="headerlink" href="#channel2" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to couple the conductance and Vm from</p>
-</dd></dl>
-
-</div></blockquote>
-<p>terminal 1 to the compartment at terminal 2. The first entry is source
-sending out Gk and Vm1, the second entry is destination for Vm2.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects. The Process should be called _second_ in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Vm1">
-<tt class="descname">Vm1</tt><big>(</big><big>)</big><a class="headerlink" href="#Vm1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles Vm message from compartment</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Vm2">
-<tt class="descname">Vm2</tt><big>(</big><big>)</big><a class="headerlink" href="#Vm2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles Vm message from another compartment</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="setGk">
-<tt class="descname">setGk</tt><big>(</big><big>)</big><a class="headerlink" href="#setGk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="getGk">
-<tt class="descname">getGk</tt><big>(</big><big>)</big><a class="headerlink" href="#getGk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">process</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘process’ call</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">reinit</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="channel1Out">
-<tt class="descname">channel1Out</tt><a class="headerlink" href="#channel1Out" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends Gk and Vm from one compartment to the other</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="channel2Out">
-<tt class="descname">channel2Out</tt><a class="headerlink" href="#channel2Out" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends Gk and Vm from one compartment to the other</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Gk">
-<tt class="descname">Gk</tt><a class="headerlink" href="#Gk" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Conductance of the gap junction</p>
-</dd></dl>
-
-</div></blockquote>
-<dl class="class">
-<dt id="Group">
-<em class="property">class </em><tt class="descname">Group</tt><a class="headerlink" href="#Group" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="Group.group">
-<tt class="descname">group</tt><a class="headerlink" href="#Group.group" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>source message field</em>) Handle for grouping Elements</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Gsolve">
-<em class="property">class </em><tt class="descname">Gsolve</tt><a class="headerlink" href="#Gsolve" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="Gsolve.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Gsolve.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.setStoich">
-<tt class="descname">setStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setStoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.getStoich">
-<tt class="descname">getStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getStoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.getNumLocalVoxels">
-<tt class="descname">getNumLocalVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getNumLocalVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.setNVec">
-<tt class="descname">setNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setNVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.getNVec">
-<tt class="descname">getNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getNVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.setNumAllVoxels">
-<tt class="descname">setNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setNumAllVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.getNumAllVoxels">
-<tt class="descname">getNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getNumAllVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.setNumPools">
-<tt class="descname">setNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setNumPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.getNumPools">
-<tt class="descname">getNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getNumPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.setUseRandInit">
-<tt class="descname">setUseRandInit</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.setUseRandInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Gsolve.getUseRandInit">
-<tt class="descname">getUseRandInit</tt><big>(</big><big>)</big><a class="headerlink" href="#Gsolve.getUseRandInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Gsolve.stoich">
-<tt class="descname">stoich</tt><a class="headerlink" href="#Gsolve.stoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Stoichiometry object for handling this reaction system.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Gsolve.numLocalVoxels">
-<tt class="descname">numLocalVoxels</tt><a class="headerlink" href="#Gsolve.numLocalVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of voxels in the core reac-diff system, on the current solver.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Gsolve.numAllVoxels">
-<tt class="descname">numAllVoxels</tt><a class="headerlink" href="#Gsolve.numAllVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of voxels in the entire reac-diff system, including proxy voxels to represent abutting compartments.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Gsolve.numPools">
-<tt class="descname">numPools</tt><a class="headerlink" href="#Gsolve.numPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Gsolve.useRandInit">
-<tt class="descname">useRandInit</tt><a class="headerlink" href="#Gsolve.useRandInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Flag: True when using probabilistic (random) rounding. When initializing the mol# from floating-point Sinit values, we have two options. One is to look at each Sinit, and round to the nearest integer. The other is to look at each Sinit, and probabilistically round up or down depending on the value. For example, if we had a Sinit value of 1.49, this would always be rounded to 1.0 if the flag is false, and would be rounded to 1.0 and 2.0 in the ratio 51:49 if the flag is true.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Gsolve.nVec">
-<tt class="descname">nVec</tt><a class="headerlink" href="#Gsolve.nVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,vector<double> (<em>lookup field</em>) vector of pool counts</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="HHChannel">
-<em class="property">class </em><tt class="descname">HHChannel</tt><a class="headerlink" href="#HHChannel" title="Permalink to this definition">¶</a></dt>
-<dd><blockquote>
-<div><p>HHChannel: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.</p>
-<dl class="attribute">
-<dt id="HHChannel.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#HHChannel.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</p>
-</dd></dl>
-
-</div></blockquote>
-<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-<blockquote>
-<div><dl class="method">
-<dt id="HHChannel.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setXpower">
-<tt class="descname">setXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setXpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getXpower">
-<tt class="descname">getXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getXpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setYpower">
-<tt class="descname">setYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setYpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getYpower">
-<tt class="descname">getYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getYpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setZpower">
-<tt class="descname">setZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setZpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getZpower">
-<tt class="descname">getZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getZpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setInstant">
-<tt class="descname">setInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setInstant" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getInstant">
-<tt class="descname">getInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getInstant" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setX">
-<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getX">
-<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setY">
-<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getY">
-<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setZ">
-<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getZ">
-<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setUseConcentration">
-<tt class="descname">setUseConcentration</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setUseConcentration" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getUseConcentration">
-<tt class="descname">getUseConcentration</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getUseConcentration" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.concen">
-<tt class="descname">concen</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.concen" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Incoming message from Concen object to specific conc to usein the Z gate calculations</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.createGate">
-<tt class="descname">createGate</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.createGate" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Function to create specified gate.Argument: Gate type [X Y Z]</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setNumGateX">
-<tt class="descname">setNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setNumGateX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getNumGateX">
-<tt class="descname">getNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getNumGateX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setNumGateY">
-<tt class="descname">setNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setNumGateY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getNumGateY">
-<tt class="descname">getNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getNumGateY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.setNumGateZ">
-<tt class="descname">setNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.setNumGateZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel.getNumGateZ">
-<tt class="descname">getNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel.getNumGateZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel.Xpower">
-<tt class="descname">Xpower</tt><a class="headerlink" href="#HHChannel.Xpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Power for X gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel.Ypower">
-<tt class="descname">Ypower</tt><a class="headerlink" href="#HHChannel.Ypower" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Power for Y gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel.Zpower">
-<tt class="descname">Zpower</tt><a class="headerlink" href="#HHChannel.Zpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Power for Z gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel.instant">
-<tt class="descname">instant</tt><a class="headerlink" href="#HHChannel.instant" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel.X">
-<tt class="descname">X</tt><a class="headerlink" href="#HHChannel.X" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) State variable for X gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel.Y">
-<tt class="descname">Y</tt><a class="headerlink" href="#HHChannel.Y" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) State variable for Y gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel.Z">
-<tt class="descname">Z</tt><a class="headerlink" href="#HHChannel.Z" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) State variable for Y gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel.useConcentration">
-<tt class="descname">useConcentration</tt><a class="headerlink" href="#HHChannel.useConcentration" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) Flag: when true, use concentration message rather than Vm tocontrol Z gate</p>
-</dd></dl>
-
-</div></blockquote>
-</dd></dl>
-
-<dl class="class">
-<dt id="HHChannel2D">
-<em class="property">class </em><tt class="descname">HHChannel2D</tt><a class="headerlink" href="#HHChannel2D" title="Permalink to this definition">¶</a></dt>
-<dd><blockquote>
-<div><p>HHChannel2D: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.</p>
-<dl class="attribute">
-<dt id="HHChannel2D.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#HHChannel2D.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</p>
-</dd></dl>
-
-</div></blockquote>
-<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-<blockquote>
-<div><dl class="method">
-<dt id="HHChannel2D.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setXindex">
-<tt class="descname">setXindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setXindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getXindex">
-<tt class="descname">getXindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getXindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setYindex">
-<tt class="descname">setYindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setYindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getYindex">
-<tt class="descname">getYindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getYindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setZindex">
-<tt class="descname">setZindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setZindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getZindex">
-<tt class="descname">getZindex</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getZindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setXpower">
-<tt class="descname">setXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setXpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getXpower">
-<tt class="descname">getXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getXpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setYpower">
-<tt class="descname">setYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setYpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getYpower">
-<tt class="descname">getYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getYpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setZpower">
-<tt class="descname">setZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setZpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getZpower">
-<tt class="descname">getZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getZpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setInstant">
-<tt class="descname">setInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setInstant" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getInstant">
-<tt class="descname">getInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getInstant" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setX">
-<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getX">
-<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setY">
-<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getY">
-<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setZ">
-<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getZ">
-<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.concen">
-<tt class="descname">concen</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.concen" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Incoming message from Concen object to specific conc to useas the first concen variable</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.concen2">
-<tt class="descname">concen2</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.concen2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Incoming message from Concen object to specific conc to useas the second concen variable</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setNumGateX">
-<tt class="descname">setNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setNumGateX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getNumGateX">
-<tt class="descname">getNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getNumGateX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setNumGateY">
-<tt class="descname">setNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setNumGateY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getNumGateY">
-<tt class="descname">getNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getNumGateY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.setNumGateZ">
-<tt class="descname">setNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.setNumGateZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHChannel2D.getNumGateZ">
-<tt class="descname">getNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#HHChannel2D.getNumGateZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.Xindex">
-<tt class="descname">Xindex</tt><a class="headerlink" href="#HHChannel2D.Xindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) String for setting X index.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.Yindex">
-<tt class="descname">Yindex</tt><a class="headerlink" href="#HHChannel2D.Yindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) String for setting Y index.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.Zindex">
-<tt class="descname">Zindex</tt><a class="headerlink" href="#HHChannel2D.Zindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) String for setting Z index.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.Xpower">
-<tt class="descname">Xpower</tt><a class="headerlink" href="#HHChannel2D.Xpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Power for X gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.Ypower">
-<tt class="descname">Ypower</tt><a class="headerlink" href="#HHChannel2D.Ypower" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Power for Y gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.Zpower">
-<tt class="descname">Zpower</tt><a class="headerlink" href="#HHChannel2D.Zpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Power for Z gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.instant">
-<tt class="descname">instant</tt><a class="headerlink" href="#HHChannel2D.instant" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.X">
-<tt class="descname">X</tt><a class="headerlink" href="#HHChannel2D.X" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) State variable for X gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.Y">
-<tt class="descname">Y</tt><a class="headerlink" href="#HHChannel2D.Y" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) State variable for Y gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHChannel2D.Z">
-<tt class="descname">Z</tt><a class="headerlink" href="#HHChannel2D.Z" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) State variable for Y gate</p>
-</dd></dl>
-
-</div></blockquote>
-</dd></dl>
-
-<dl class="class">
-<dt id="HHGate">
-<em class="property">class </em><tt class="descname">HHGate</tt><a class="headerlink" href="#HHGate" title="Permalink to this definition">¶</a></dt>
-<dd><p>HHGate: Gate for Hodkgin-Huxley type channels, equivalent to the m and h terms on the Na squid channel and the n term on K. This takes the voltage and state variable from the channel, computes the new value of the state variable and a scaling, depending on gate power, for the conductance.</p>
-<dl class="method">
-<dt id="HHGate.getA">
-<tt class="descname">getA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getB">
-<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setAlpha">
-<tt class="descname">setAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setAlpha" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getAlpha">
-<tt class="descname">getAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getAlpha" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setBeta">
-<tt class="descname">setBeta</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setBeta" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getBeta">
-<tt class="descname">getBeta</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getBeta" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setTau">
-<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getTau">
-<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setMInfinity">
-<tt class="descname">setMInfinity</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setMInfinity" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getMInfinity">
-<tt class="descname">getMInfinity</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getMInfinity" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setMin">
-<tt class="descname">setMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setMin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getMin">
-<tt class="descname">getMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getMin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setMax">
-<tt class="descname">setMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setMax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getMax">
-<tt class="descname">getMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getMax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setDivs">
-<tt class="descname">setDivs</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setDivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getDivs">
-<tt class="descname">getDivs</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getDivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setTableA">
-<tt class="descname">setTableA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setTableA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getTableA">
-<tt class="descname">getTableA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getTableA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setTableB">
-<tt class="descname">setTableB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setTableB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getTableB">
-<tt class="descname">getTableB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getTableB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setUseInterpolation">
-<tt class="descname">setUseInterpolation</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setUseInterpolation" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getUseInterpolation">
-<tt class="descname">getUseInterpolation</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getUseInterpolation" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setAlphaParms">
-<tt class="descname">setAlphaParms</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setAlphaParms" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.getAlphaParms">
-<tt class="descname">getAlphaParms</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.getAlphaParms" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setupAlpha">
-<tt class="descname">setupAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setupAlpha" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setupTau">
-<tt class="descname">setupTau</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setupTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Identical to setupAlpha, except that the forms specified bythe 13 parameters are for the tau and m-infinity curves ratherthan the alpha and beta terms. So the parameters are:setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmaxAs before, the equation describing each curve is:y(x) = (A + B * x) / (C + exp((x + D) / F))</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.tweakAlpha">
-<tt class="descname">tweakAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.tweakAlpha" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Dummy function for backward compatibility. It used to convertthe tables from alpha, beta values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.tweakTau">
-<tt class="descname">tweakTau</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.tweakTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Dummy function for backward compatibility. It used to convertthe tables from tau, minf values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate.setupGate">
-<tt class="descname">setupGate</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate.setupGate" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Sets up one gate at a time using the alpha/beta form.Has 9 parameters, as follows:setupGate A B C D F xdivs xmin xmax is_betaThis sets up the gate using the equation:y(x) = (A + B * x) / (C + exp((x + D) / F))Deprecated.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.alpha">
-<tt class="descname">alpha</tt><a class="headerlink" href="#HHGate.alpha" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Parameters for voltage-dependent rates, alpha:Set up alpha term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.beta">
-<tt class="descname">beta</tt><a class="headerlink" href="#HHGate.beta" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Parameters for voltage-dependent rates, beta:Set up beta term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.tau">
-<tt class="descname">tau</tt><a class="headerlink" href="#HHGate.tau" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Parameters for voltage-dependent rates, tau:Set up tau curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.mInfinity">
-<tt class="descname">mInfinity</tt><a class="headerlink" href="#HHGate.mInfinity" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Parameters for voltage-dependent rates, mInfinity:Set up mInfinity curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.min">
-<tt class="descname">min</tt><a class="headerlink" href="#HHGate.min" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.max">
-<tt class="descname">max</tt><a class="headerlink" href="#HHGate.max" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.divs">
-<tt class="descname">divs</tt><a class="headerlink" href="#HHGate.divs" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.tableA">
-<tt class="descname">tableA</tt><a class="headerlink" href="#HHGate.tableA" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Table of A entries</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.tableB">
-<tt class="descname">tableB</tt><a class="headerlink" href="#HHGate.tableB" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Table of alpha + beta entries</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.useInterpolation">
-<tt class="descname">useInterpolation</tt><a class="headerlink" href="#HHGate.useInterpolation" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Flag: use linear interpolation if true, else direct lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.alphaParms">
-<tt class="descname">alphaParms</tt><a class="headerlink" href="#HHGate.alphaParms" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.A">
-<tt class="descname">A</tt><a class="headerlink" href="#HHGate.A" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>lookup field</em>) lookupA: Look up the A gate value from a double. Usually doesso by direct scaling and offset to an integer lookup, usinga fine enough table granularity that there is little error.Alternatively uses linear interpolation.The range of the double is predefined based on knowledge ofvoltage or conc ranges, and the granularity is specified bythe xmin, xmax, and dV fields.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate.B">
-<tt class="descname">B</tt><a class="headerlink" href="#HHGate.B" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>lookup field</em>) lookupB: Look up the B gate value from a double.Note that this looks up the raw tables, which are transformedfrom the reference parameters.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="HHGate2D">
-<em class="property">class </em><tt class="descname">HHGate2D</tt><a class="headerlink" href="#HHGate2D" title="Permalink to this definition">¶</a></dt>
-<dd><p>HHGate2D: Gate for Hodkgin-Huxley type channels, equivalent to the m and h terms on the Na squid channel and the n term on K. This takes the voltage and state variable from the channel, computes the new value of the state variable and a scaling, depending on gate power, for the conductance. These two terms are sent right back in a message to the channel.</p>
-<dl class="method">
-<dt id="HHGate2D.getA">
-<tt class="descname">getA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getB">
-<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setTableA">
-<tt class="descname">setTableA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setTableA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getTableA">
-<tt class="descname">getTableA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getTableA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setTableB">
-<tt class="descname">setTableB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setTableB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getTableB">
-<tt class="descname">getTableB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getTableB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setXminA">
-<tt class="descname">setXminA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXminA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getXminA">
-<tt class="descname">getXminA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXminA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setXmaxA">
-<tt class="descname">setXmaxA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXmaxA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getXmaxA">
-<tt class="descname">getXmaxA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXmaxA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setXdivsA">
-<tt class="descname">setXdivsA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXdivsA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getXdivsA">
-<tt class="descname">getXdivsA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXdivsA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setYminA">
-<tt class="descname">setYminA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYminA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getYminA">
-<tt class="descname">getYminA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYminA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setYmaxA">
-<tt class="descname">setYmaxA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYmaxA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getYmaxA">
-<tt class="descname">getYmaxA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYmaxA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setYdivsA">
-<tt class="descname">setYdivsA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYdivsA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getYdivsA">
-<tt class="descname">getYdivsA</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYdivsA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setXminB">
-<tt class="descname">setXminB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXminB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getXminB">
-<tt class="descname">getXminB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXminB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setXmaxB">
-<tt class="descname">setXmaxB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXmaxB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getXmaxB">
-<tt class="descname">getXmaxB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXmaxB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setXdivsB">
-<tt class="descname">setXdivsB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setXdivsB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getXdivsB">
-<tt class="descname">getXdivsB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getXdivsB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setYminB">
-<tt class="descname">setYminB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYminB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getYminB">
-<tt class="descname">getYminB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYminB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setYmaxB">
-<tt class="descname">setYmaxB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYmaxB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getYmaxB">
-<tt class="descname">getYmaxB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYmaxB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.setYdivsB">
-<tt class="descname">setYdivsB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.setYdivsB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HHGate2D.getYdivsB">
-<tt class="descname">getYdivsB</tt><big>(</big><big>)</big><a class="headerlink" href="#HHGate2D.getYdivsB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.tableA">
-<tt class="descname">tableA</tt><a class="headerlink" href="#HHGate2D.tableA" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector< vector<double> > (<em>value field</em>) Table of A entries</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.tableB">
-<tt class="descname">tableB</tt><a class="headerlink" href="#HHGate2D.tableB" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector< vector<double> > (<em>value field</em>) Table of B entries</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.xminA">
-<tt class="descname">xminA</tt><a class="headerlink" href="#HHGate2D.xminA" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.xmaxA">
-<tt class="descname">xmaxA</tt><a class="headerlink" href="#HHGate2D.xmaxA" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.xdivsA">
-<tt class="descname">xdivsA</tt><a class="headerlink" href="#HHGate2D.xdivsA" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.yminA">
-<tt class="descname">yminA</tt><a class="headerlink" href="#HHGate2D.yminA" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.ymaxA">
-<tt class="descname">ymaxA</tt><a class="headerlink" href="#HHGate2D.ymaxA" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.ydivsA">
-<tt class="descname">ydivsA</tt><a class="headerlink" href="#HHGate2D.ydivsA" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.xminB">
-<tt class="descname">xminB</tt><a class="headerlink" href="#HHGate2D.xminB" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.xmaxB">
-<tt class="descname">xmaxB</tt><a class="headerlink" href="#HHGate2D.xmaxB" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.xdivsB">
-<tt class="descname">xdivsB</tt><a class="headerlink" href="#HHGate2D.xdivsB" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.yminB">
-<tt class="descname">yminB</tt><a class="headerlink" href="#HHGate2D.yminB" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.ymaxB">
-<tt class="descname">ymaxB</tt><a class="headerlink" href="#HHGate2D.ymaxB" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum range for lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.ydivsB">
-<tt class="descname">ydivsB</tt><a class="headerlink" href="#HHGate2D.ydivsB" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Divisions for lookup. Zero means to use linear interpolation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.A">
-<tt class="descname">A</tt><a class="headerlink" href="#HHGate2D.A" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double>,double (<em>lookup field</em>) lookupA: Look up the A gate value from two doubles, passedin as a vector. Uses linear interpolation in the 2D tableThe range of the lookup doubles is predefined based on knowledge of voltage or conc ranges, and the granularity is specified by the xmin, xmax, and dx field, and their y-axis counterparts.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HHGate2D.B">
-<tt class="descname">B</tt><a class="headerlink" href="#HHGate2D.B" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double>,double (<em>lookup field</em>) lookupB: Look up B gate value from two doubles in a vector.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="HSolve">
-<em class="property">class </em><tt class="descname">HSolve</tt><a class="headerlink" href="#HSolve" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="HSolve.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#HSolve.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Handles ‘reinit’ and ‘process’ calls from a clock.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setSeed">
-<tt class="descname">setSeed</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setSeed" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getSeed">
-<tt class="descname">getSeed</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getSeed" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setTarget">
-<tt class="descname">setTarget</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setTarget" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getTarget">
-<tt class="descname">getTarget</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getTarget" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setDt">
-<tt class="descname">setDt</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getDt">
-<tt class="descname">getDt</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setCaAdvance">
-<tt class="descname">setCaAdvance</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setCaAdvance" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getCaAdvance">
-<tt class="descname">getCaAdvance</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getCaAdvance" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setVDiv">
-<tt class="descname">setVDiv</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setVDiv" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getVDiv">
-<tt class="descname">getVDiv</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getVDiv" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setVMin">
-<tt class="descname">setVMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setVMin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getVMin">
-<tt class="descname">getVMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getVMin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setVMax">
-<tt class="descname">setVMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setVMax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getVMax">
-<tt class="descname">getVMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getVMax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setCaDiv">
-<tt class="descname">setCaDiv</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setCaDiv" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getCaDiv">
-<tt class="descname">getCaDiv</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getCaDiv" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setCaMin">
-<tt class="descname">setCaMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setCaMin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getCaMin">
-<tt class="descname">getCaMin</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getCaMin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.setCaMax">
-<tt class="descname">setCaMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.setCaMax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.getCaMax">
-<tt class="descname">getCaMax</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.getCaMax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘process’ call: Solver advances by one time-step.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="HSolve.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#HSolve.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call: Solver reads in model.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.seed">
-<tt class="descname">seed</tt><a class="headerlink" href="#HSolve.seed" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Use this field to specify path to a ‘seed’ compartment, that is, any compartment within a neuron. The HSolve object uses this seed as a handle to discover the rest of the neuronal model, which means all the remaining compartments, channels, synapses, etc.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.target">
-<tt class="descname">target</tt><a class="headerlink" href="#HSolve.target" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Specifies the path to a compartmental model to be taken over. This can be the path to any container object that has the model under it (found by performing a deep search). Alternatively, this can also be the path to any compartment within the neuron. This compartment will be used as a handle to discover the rest of the model, which means all the remaining compartments, channels, synapses, etc.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.dt">
-<tt class="descname">dt</tt><a class="headerlink" href="#HSolve.dt" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) The time-step for this solver.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.caAdvance">
-<tt class="descname">caAdvance</tt><a class="headerlink" href="#HSolve.caAdvance" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) This flag determines how current flowing into a calcium pool is computed. A value of 0 means that the membrane potential at the beginning of the time-step is used for the calculation. This is how GENESIS does its computations. A value of 1 means the membrane potential at the middle of the time-step is used. This is the correct way of integration, and is the default way.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.vDiv">
-<tt class="descname">vDiv</tt><a class="headerlink" href="#HSolve.vDiv" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) Specifies number of divisions for lookup tables of voltage-sensitive channels.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.vMin">
-<tt class="descname">vMin</tt><a class="headerlink" href="#HSolve.vMin" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Specifies the lower bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.vMax">
-<tt class="descname">vMax</tt><a class="headerlink" href="#HSolve.vMax" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Specifies the upper bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.caDiv">
-<tt class="descname">caDiv</tt><a class="headerlink" href="#HSolve.caDiv" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) Specifies number of divisions for lookup tables of calcium-sensitive channels.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.caMin">
-<tt class="descname">caMin</tt><a class="headerlink" href="#HSolve.caMin" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Specifies the lower bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="HSolve.caMax">
-<tt class="descname">caMax</tt><a class="headerlink" href="#HSolve.caMax" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Specifies the upper bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="IntFire">
-<em class="property">class </em><tt class="descname">IntFire</tt><a class="headerlink" href="#IntFire" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="IntFire.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#IntFire.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.setVm">
-<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.getVm">
-<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.setTau">
-<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.getTau">
-<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.setThresh">
-<tt class="descname">setThresh</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setThresh" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.getThresh">
-<tt class="descname">getThresh</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getThresh" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.setRefractoryPeriod">
-<tt class="descname">setRefractoryPeriod</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setRefractoryPeriod" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.getRefractoryPeriod">
-<tt class="descname">getRefractoryPeriod</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getRefractoryPeriod" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.setBufferTime">
-<tt class="descname">setBufferTime</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.setBufferTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.getBufferTime">
-<tt class="descname">getBufferTime</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.getBufferTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IntFire.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#IntFire.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IntFire.spikeOut">
-<tt class="descname">spikeOut</tt><a class="headerlink" href="#IntFire.spikeOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out spike events</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IntFire.Vm">
-<tt class="descname">Vm</tt><a class="headerlink" href="#IntFire.Vm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Membrane potential</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IntFire.tau">
-<tt class="descname">tau</tt><a class="headerlink" href="#IntFire.tau" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) charging time-course</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IntFire.thresh">
-<tt class="descname">thresh</tt><a class="headerlink" href="#IntFire.thresh" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) firing threshold</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IntFire.refractoryPeriod">
-<tt class="descname">refractoryPeriod</tt><a class="headerlink" href="#IntFire.refractoryPeriod" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum time between successive spikes</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IntFire.bufferTime">
-<tt class="descname">bufferTime</tt><a class="headerlink" href="#IntFire.bufferTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Duration of spike buffer.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Interpol">
-<em class="property">class </em><tt class="descname">Interpol</tt><a class="headerlink" href="#Interpol" title="Permalink to this definition">¶</a></dt>
-<dd><p>Interpol: Interpolation class. Handles lookup from a 1-dimensional array of real-numbered values.Returns ‘y’ value based on given ‘x’ value. Can either use interpolation or roundoff to the nearest index.</p>
-<dl class="attribute">
-<dt id="Interpol.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Interpol.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol.setXmin">
-<tt class="descname">setXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.setXmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol.getXmin">
-<tt class="descname">getXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.getXmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol.setXmax">
-<tt class="descname">setXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.setXmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol.getXmax">
-<tt class="descname">getXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.getXmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol.getY">
-<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.getY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol.input">
-<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.input" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Interpolates using the input as x value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol.lookupOut">
-<tt class="descname">lookupOut</tt><a class="headerlink" href="#Interpol.lookupOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) respond to a request for a value lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol.xmin">
-<tt class="descname">xmin</tt><a class="headerlink" href="#Interpol.xmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum value of x. x below this will result in y[0] being returned.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol.xmax">
-<tt class="descname">xmax</tt><a class="headerlink" href="#Interpol.xmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximum value of x. x above this will result in y[last] being returned.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol.y">
-<tt class="descname">y</tt><a class="headerlink" href="#Interpol.y" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Looked up value.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Interpol2D">
-<em class="property">class </em><tt class="descname">Interpol2D</tt><a class="headerlink" href="#Interpol2D" title="Permalink to this definition">¶</a></dt>
-<dd><p>Interpol2D: Interpolation class. Handles lookup from a 2-dimensional grid of real-numbered values. Returns ‘z’ value based on given ‘x’ and ‘y’ values. Can either use interpolation or roundoff to the nearest index.</p>
-<dl class="attribute">
-<dt id="Interpol2D.lookupReturn2D">
-<tt class="descname">lookupReturn2D</tt><a class="headerlink" href="#Interpol2D.lookupReturn2D" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message for doing lookups on the table. Receives 2 doubles: x, y. Sends back a double with the looked-up z value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.lookup">
-<tt class="descname">lookup</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.lookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Looks up table value based on indices v1 and v2, and sendsvalue back using the ‘lookupOut’ message</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setXmin">
-<tt class="descname">setXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setXmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getXmin">
-<tt class="descname">getXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getXmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setXmax">
-<tt class="descname">setXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setXmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getXmax">
-<tt class="descname">getXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getXmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setXdivs">
-<tt class="descname">setXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setXdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getXdivs">
-<tt class="descname">getXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getXdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setDx">
-<tt class="descname">setDx</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setDx" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getDx">
-<tt class="descname">getDx</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getDx" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setYmin">
-<tt class="descname">setYmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setYmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getYmin">
-<tt class="descname">getYmin</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getYmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setYmax">
-<tt class="descname">setYmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setYmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getYmax">
-<tt class="descname">getYmax</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getYmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setYdivs">
-<tt class="descname">setYdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setYdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getYdivs">
-<tt class="descname">getYdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getYdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setDy">
-<tt class="descname">setDy</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setDy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getDy">
-<tt class="descname">getDy</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getDy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setTable">
-<tt class="descname">setTable</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setTable" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getTable">
-<tt class="descname">getTable</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getTable" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getZ">
-<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.setTableVector2D">
-<tt class="descname">setTableVector2D</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.setTableVector2D" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Interpol2D.getTableVector2D">
-<tt class="descname">getTableVector2D</tt><big>(</big><big>)</big><a class="headerlink" href="#Interpol2D.getTableVector2D" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.lookupOut">
-<tt class="descname">lookupOut</tt><a class="headerlink" href="#Interpol2D.lookupOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) respond to a request for a value lookup</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.xmin">
-<tt class="descname">xmin</tt><a class="headerlink" href="#Interpol2D.xmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum value for x axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.xmax">
-<tt class="descname">xmax</tt><a class="headerlink" href="#Interpol2D.xmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximum value for x axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.xdivs">
-<tt class="descname">xdivs</tt><a class="headerlink" href="#Interpol2D.xdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) # of divisions on x axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.dx">
-<tt class="descname">dx</tt><a class="headerlink" href="#Interpol2D.dx" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Increment on x axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.ymin">
-<tt class="descname">ymin</tt><a class="headerlink" href="#Interpol2D.ymin" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum value for y axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.ymax">
-<tt class="descname">ymax</tt><a class="headerlink" href="#Interpol2D.ymax" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximum value for y axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.ydivs">
-<tt class="descname">ydivs</tt><a class="headerlink" href="#Interpol2D.ydivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) # of divisions on y axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.dy">
-<tt class="descname">dy</tt><a class="headerlink" href="#Interpol2D.dy" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Increment on y axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.tableVector2D">
-<tt class="descname">tableVector2D</tt><a class="headerlink" href="#Interpol2D.tableVector2D" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector< vector<double> > (<em>value field</em>) Get the entire table.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.table">
-<tt class="descname">table</tt><a class="headerlink" href="#Interpol2D.table" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int>,double (<em>lookup field</em>) Lookup an entry on the table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Interpol2D.z">
-<tt class="descname">z</tt><a class="headerlink" href="#Interpol2D.z" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double>,double (<em>lookup field</em>) Interpolated value for specified x and y. This is provided for debugging. Normally other objects will retrieve interpolated values via lookup message.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="IzhikevichNrn">
-<em class="property">class </em><tt class="descname">IzhikevichNrn</tt><a class="headerlink" href="#IzhikevichNrn" title="Permalink to this definition">¶</a></dt>
-<dd><p>Izhikevich model of spiking neuron (Izhikevich,EM. 2003. Simple model of spiking neurons. Neural Networks, IEEE Transactions on 14(6). pp 1569-1572).</p>
-<blockquote>
-<div><blockquote>
-<div><p>dVm/dt = 0.04 * Vm^2 + 5 * Vm + 140 - u + inject</p>
-<p>du/dt = a * (b * Vm - u)</p>
-</div></blockquote>
-<p>if Vm >= Vmax then Vm = c and u = u + d</p>
-<p>Vmax = 30 mV in the paper.</p>
-</div></blockquote>
-<dl class="attribute">
-<dt id="IzhikevichNrn.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#IzhikevichNrn.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.channel">
-<tt class="descname">channel</tt><a class="headerlink" href="#IzhikevichNrn.channel" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message from a IzhikevichNrn to channels.The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setVmax">
-<tt class="descname">setVmax</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setVmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getVmax">
-<tt class="descname">getVmax</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getVmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setC">
-<tt class="descname">setC</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setC" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getC">
-<tt class="descname">getC</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getC" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setD">
-<tt class="descname">setD</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setD" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getD">
-<tt class="descname">getD</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getD" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setA">
-<tt class="descname">setA</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getA">
-<tt class="descname">getA</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getA" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setB">
-<tt class="descname">setB</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getB">
-<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getU">
-<tt class="descname">getU</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getU" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setVm">
-<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getVm">
-<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getIm">
-<tt class="descname">getIm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getIm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setInject">
-<tt class="descname">setInject</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setInject" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getInject">
-<tt class="descname">getInject</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getInject" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setRmByTau">
-<tt class="descname">setRmByTau</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setRmByTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getRmByTau">
-<tt class="descname">getRmByTau</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getRmByTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setAccommodating">
-<tt class="descname">setAccommodating</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setAccommodating" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getAccommodating">
-<tt class="descname">getAccommodating</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getAccommodating" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setU0">
-<tt class="descname">setU0</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setU0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getU0">
-<tt class="descname">getU0</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getU0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setInitVm">
-<tt class="descname">setInitVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setInitVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getInitVm">
-<tt class="descname">getInitVm</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getInitVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setInitU">
-<tt class="descname">setInitU</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setInitU" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getInitU">
-<tt class="descname">getInitU</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getInitU" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setAlpha">
-<tt class="descname">setAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setAlpha" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getAlpha">
-<tt class="descname">getAlpha</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getAlpha" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setBeta">
-<tt class="descname">setBeta</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setBeta" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getBeta">
-<tt class="descname">getBeta</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getBeta" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.setGamma">
-<tt class="descname">setGamma</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.setGamma" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.getGamma">
-<tt class="descname">getGamma</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.getGamma" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.injectMsg">
-<tt class="descname">injectMsg</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.injectMsg" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Injection current into the neuron.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.cDest">
-<tt class="descname">cDest</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.cDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Destination message to modify parameter c at runtime.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.dDest">
-<tt class="descname">dDest</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.dDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Destination message to modify parameter d at runtime.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.bDest">
-<tt class="descname">bDest</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.bDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Destination message to modify parameter b at runtime</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.aDest">
-<tt class="descname">aDest</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.aDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Destination message modify parameter a at runtime.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="IzhikevichNrn.handleChannel">
-<tt class="descname">handleChannel</tt><big>(</big><big>)</big><a class="headerlink" href="#IzhikevichNrn.handleChannel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles conductance and reversal potential arguments from Channel</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.VmOut">
-<tt class="descname">VmOut</tt><a class="headerlink" href="#IzhikevichNrn.VmOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out Vm</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.spikeOut">
-<tt class="descname">spikeOut</tt><a class="headerlink" href="#IzhikevichNrn.spikeOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out spike events</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt>
-<tt class="descname">VmOut</tt></dt>
-<dd><p>double (<em>source message field</em>) Sends out Vm</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.Vmax">
-<tt class="descname">Vmax</tt><a class="headerlink" href="#IzhikevichNrn.Vmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximum membrane potential. Membrane potential is reset to c whenever it reaches Vmax. NOTE: Izhikevich model specifies the PEAK voltage, rather than THRSHOLD voltage. The threshold depends on the previous history.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.c">
-<tt class="descname">c</tt><a class="headerlink" href="#IzhikevichNrn.c" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Reset potential. Membrane potential is reset to c whenever it reaches Vmax.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.d">
-<tt class="descname">d</tt><a class="headerlink" href="#IzhikevichNrn.d" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Parameter d in Izhikevich model. Unit is V/s.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.a">
-<tt class="descname">a</tt><a class="headerlink" href="#IzhikevichNrn.a" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Parameter a in Izhikevich model. Unit is s^{-1}</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.b">
-<tt class="descname">b</tt><a class="headerlink" href="#IzhikevichNrn.b" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Parameter b in Izhikevich model. Unit is s^{-1}</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.u">
-<tt class="descname">u</tt><a class="headerlink" href="#IzhikevichNrn.u" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Parameter u in Izhikevich equation. Unit is V/s</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.Vm">
-<tt class="descname">Vm</tt><a class="headerlink" href="#IzhikevichNrn.Vm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Membrane potential, equivalent to v in Izhikevich equation.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.Im">
-<tt class="descname">Im</tt><a class="headerlink" href="#IzhikevichNrn.Im" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Total current going through the membrane. Unit is A.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.inject">
-<tt class="descname">inject</tt><a class="headerlink" href="#IzhikevichNrn.inject" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) External current injection into the neuron</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.RmByTau">
-<tt class="descname">RmByTau</tt><a class="headerlink" href="#IzhikevichNrn.RmByTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Hidden coefficient of input current term (I) in Izhikevich model. Defaults to 1e9 Ohm/s.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.accommodating">
-<tt class="descname">accommodating</tt><a class="headerlink" href="#IzhikevichNrn.accommodating" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) True if this neuron is an accommodating one. The equation for recovery variable u is special in this case.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.u0">
-<tt class="descname">u0</tt><a class="headerlink" href="#IzhikevichNrn.u0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) This is used for accommodating neurons where recovery variables u is computed as: u += tau*a*(b*(Vm-u0))</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.initVm">
-<tt class="descname">initVm</tt><a class="headerlink" href="#IzhikevichNrn.initVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Initial membrane potential. Unit is V.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.initU">
-<tt class="descname">initU</tt><a class="headerlink" href="#IzhikevichNrn.initU" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Initial value of u.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.alpha">
-<tt class="descname">alpha</tt><a class="headerlink" href="#IzhikevichNrn.alpha" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Coefficient of v^2 in Izhikevich equation. Defaults to 0.04 in physiological unit. In SI it should be 40000.0. Unit is V^-1 s^{-1}</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.beta">
-<tt class="descname">beta</tt><a class="headerlink" href="#IzhikevichNrn.beta" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Coefficient of v in Izhikevich model. Defaults to 5 in physiological unit, 5000.0 for SI units. Unit is s^{-1}</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="IzhikevichNrn.gamma">
-<tt class="descname">gamma</tt><a class="headerlink" href="#IzhikevichNrn.gamma" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Constant term in Izhikevich model. Defaults to 140 in both physiological and SI units. unit is V/s.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Ksolve">
-<em class="property">class </em><tt class="descname">Ksolve</tt><a class="headerlink" href="#Ksolve" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="Ksolve.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Ksolve.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.setMethod">
-<tt class="descname">setMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setMethod" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getMethod">
-<tt class="descname">getMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getMethod" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.setEpsAbs">
-<tt class="descname">setEpsAbs</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setEpsAbs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getEpsAbs">
-<tt class="descname">getEpsAbs</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getEpsAbs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.setEpsRel">
-<tt class="descname">setEpsRel</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setEpsRel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getEpsRel">
-<tt class="descname">getEpsRel</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getEpsRel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.setStoich">
-<tt class="descname">setStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setStoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getStoich">
-<tt class="descname">getStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getStoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.setDsolve">
-<tt class="descname">setDsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setDsolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getDsolve">
-<tt class="descname">getDsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getDsolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.setCompartment">
-<tt class="descname">setCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setCompartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getCompartment">
-<tt class="descname">getCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getCompartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getNumLocalVoxels">
-<tt class="descname">getNumLocalVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getNumLocalVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.setNVec">
-<tt class="descname">setNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setNVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getNVec">
-<tt class="descname">getNVec</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getNVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.setNumAllVoxels">
-<tt class="descname">setNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setNumAllVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getNumAllVoxels">
-<tt class="descname">getNumAllVoxels</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getNumAllVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.setNumPools">
-<tt class="descname">setNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.setNumPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.getNumPools">
-<tt class="descname">getNumPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.getNumPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Ksolve.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Ksolve.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.method">
-<tt class="descname">method</tt><a class="headerlink" href="#Ksolve.method" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Integration method, using GSL. So far only explict. Options are:rk5: The default Runge-Kutta-Fehlberg 5th order adaptive dt methodgsl: alias for the aboverk4: The Runge-Kutta 4th order fixed dt methodrk2: The Runge-Kutta 2,3 embedded fixed dt methodrkck: The Runge-Kutta Cash-Karp (4,5) methodrk8: The Runge-Kutta Prince-Dormand (8,9) method</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.epsAbs">
-<tt class="descname">epsAbs</tt><a class="headerlink" href="#Ksolve.epsAbs" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Absolute permissible integration error range.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.epsRel">
-<tt class="descname">epsRel</tt><a class="headerlink" href="#Ksolve.epsRel" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Relative permissible integration error range.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.stoich">
-<tt class="descname">stoich</tt><a class="headerlink" href="#Ksolve.stoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Stoichiometry object for handling this reaction system.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.dsolve">
-<tt class="descname">dsolve</tt><a class="headerlink" href="#Ksolve.dsolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Diffusion solver object handling this reactin system.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.compartment">
-<tt class="descname">compartment</tt><a class="headerlink" href="#Ksolve.compartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Compartment in which the Ksolve reaction system lives.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.numLocalVoxels">
-<tt class="descname">numLocalVoxels</tt><a class="headerlink" href="#Ksolve.numLocalVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of voxels in the core reac-diff system, on the current solver.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.numAllVoxels">
-<tt class="descname">numAllVoxels</tt><a class="headerlink" href="#Ksolve.numAllVoxels" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of voxels in the entire reac-diff system, including proxy voxels to represent abutting compartments.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.numPools">
-<tt class="descname">numPools</tt><a class="headerlink" href="#Ksolve.numPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Ksolve.nVec">
-<tt class="descname">nVec</tt><a class="headerlink" href="#Ksolve.nVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,vector<double> (<em>lookup field</em>) vector of pool counts. Index specifies which voxel.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Leakage">
-<em class="property">class </em><tt class="descname">Leakage</tt><a class="headerlink" href="#Leakage" title="Permalink to this definition">¶</a></dt>
-<dd><p>Leakage: Passive leakage channel.</p>
-<dl class="attribute">
-<dt id="Leakage.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Leakage.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from the scheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on.</p>
-</dd></dl>
-
-</dd></dl>
-
-<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-<blockquote>
-<div><dl class="method">
-<dt>
-<tt class="descname">process</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">reinit</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-</div></blockquote>
-<dl class="class">
-<dt id="Long">
-<em class="property">class </em><tt class="descname">Long</tt><a class="headerlink" href="#Long" title="Permalink to this definition">¶</a></dt>
-<dd><p>Variable for storing values.</p>
-<dl class="method">
-<dt id="Long.setValue">
-<tt class="descname">setValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Long.setValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Long.getValue">
-<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Long.getValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Long.value">
-<tt class="descname">value</tt><a class="headerlink" href="#Long.value" title="Permalink to this definition">¶</a></dt>
-<dd><p>long (<em>value field</em>) Variable value</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="MMenz">
-<em class="property">class </em><tt class="descname">MMenz</tt><a class="headerlink" href="#MMenz" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="MarkovChannel">
-<em class="property">class </em><tt class="descname">MarkovChannel</tt><a class="headerlink" href="#MarkovChannel" title="Permalink to this definition">¶</a></dt>
-<dd><p>MarkovChannel : Multistate ion channel class.It deals with ion channels which can be found in one of multiple states, some of which are conducting. This implementation assumes the occurence of first order kinetics to calculate the probabilities of the channel being found in all states. Further, the rates of transition between these states can be constant, voltage-dependent or ligand dependent (only one ligand species). The current flow obtained from the channel is calculated in a deterministic method by solving the system of differential equations obtained from the assumptions above.</p>
-<dl class="attribute">
-<dt id="MarkovChannel.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#MarkovChannel.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.setLigandConc">
-<tt class="descname">setLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setLigandConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.getLigandConc">
-<tt class="descname">getLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getLigandConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.setVm">
-<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.getVm">
-<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.setNumStates">
-<tt class="descname">setNumStates</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setNumStates" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.getNumStates">
-<tt class="descname">getNumStates</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getNumStates" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.setNumOpenStates">
-<tt class="descname">setNumOpenStates</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setNumOpenStates" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.getNumOpenStates">
-<tt class="descname">getNumOpenStates</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getNumOpenStates" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.getState">
-<tt class="descname">getState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getState" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.setInitialState">
-<tt class="descname">setInitialState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setInitialState" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.getInitialState">
-<tt class="descname">getInitialState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getInitialState" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.setLabels">
-<tt class="descname">setLabels</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setLabels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.getLabels">
-<tt class="descname">getLabels</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getLabels" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.setGbar">
-<tt class="descname">setGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.setGbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.getGbar">
-<tt class="descname">getGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.getGbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.handleLigandConc">
-<tt class="descname">handleLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.handleLigandConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Deals with incoming messages containing information of ligand concentration</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovChannel.handleState">
-<tt class="descname">handleState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovChannel.handleState" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Deals with incoming message from MarkovSolver object containing state information of the channel.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovChannel.ligandConc">
-<tt class="descname">ligandConc</tt><a class="headerlink" href="#MarkovChannel.ligandConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Ligand concentration.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovChannel.Vm">
-<tt class="descname">Vm</tt><a class="headerlink" href="#MarkovChannel.Vm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Membrane voltage.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovChannel.numStates">
-<tt class="descname">numStates</tt><a class="headerlink" href="#MarkovChannel.numStates" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) The number of states that the channel can occupy.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovChannel.numOpenStates">
-<tt class="descname">numOpenStates</tt><a class="headerlink" href="#MarkovChannel.numOpenStates" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) The number of states which are open/conducting.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovChannel.state">
-<tt class="descname">state</tt><a class="headerlink" href="#MarkovChannel.state" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) This is a row vector that contains the probabilities of finding the channel in each state.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovChannel.initialState">
-<tt class="descname">initialState</tt><a class="headerlink" href="#MarkovChannel.initialState" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) This is a row vector that contains the probabilities of finding the channel in each state at t = 0. The state of the channel is reset to this value during a call to reinit()</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovChannel.labels">
-<tt class="descname">labels</tt><a class="headerlink" href="#MarkovChannel.labels" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) Labels for each state.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovChannel.gbar">
-<tt class="descname">gbar</tt><a class="headerlink" href="#MarkovChannel.gbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) A row vector containing the conductance associated with each of the open/conducting states.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="MarkovGslSolver">
-<em class="property">class </em><tt class="descname">MarkovGslSolver</tt><a class="headerlink" href="#MarkovGslSolver" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="MarkovGslSolver.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#MarkovGslSolver.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.getIsInitialized">
-<tt class="descname">getIsInitialized</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getIsInitialized" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.setMethod">
-<tt class="descname">setMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.setMethod" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.getMethod">
-<tt class="descname">getMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getMethod" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.setRelativeAccuracy">
-<tt class="descname">setRelativeAccuracy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.setRelativeAccuracy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.getRelativeAccuracy">
-<tt class="descname">getRelativeAccuracy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getRelativeAccuracy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.setAbsoluteAccuracy">
-<tt class="descname">setAbsoluteAccuracy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.setAbsoluteAccuracy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.getAbsoluteAccuracy">
-<tt class="descname">getAbsoluteAccuracy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getAbsoluteAccuracy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.setInternalDt">
-<tt class="descname">setInternalDt</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.setInternalDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.getInternalDt">
-<tt class="descname">getInternalDt</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.getInternalDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.init">
-<tt class="descname">init</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.init" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Initialize solver parameters.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.handleQ">
-<tt class="descname">handleQ</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.handleQ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles information regarding the instantaneous rate matrix from the MarkovRateTable class.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovGslSolver.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovGslSolver.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovGslSolver.stateOut">
-<tt class="descname">stateOut</tt><a class="headerlink" href="#MarkovGslSolver.stateOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>source message field</em>) Sends updated state to the MarkovChannel class.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovGslSolver.isInitialized">
-<tt class="descname">isInitialized</tt><a class="headerlink" href="#MarkovGslSolver.isInitialized" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) True if the message has come in to set solver parameters.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovGslSolver.method">
-<tt class="descname">method</tt><a class="headerlink" href="#MarkovGslSolver.method" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Numerical method to use.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovGslSolver.relativeAccuracy">
-<tt class="descname">relativeAccuracy</tt><a class="headerlink" href="#MarkovGslSolver.relativeAccuracy" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Accuracy criterion</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovGslSolver.absoluteAccuracy">
-<tt class="descname">absoluteAccuracy</tt><a class="headerlink" href="#MarkovGslSolver.absoluteAccuracy" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Another accuracy criterion</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovGslSolver.internalDt">
-<tt class="descname">internalDt</tt><a class="headerlink" href="#MarkovGslSolver.internalDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) internal timestep to use.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="MarkovRateTable">
-<em class="property">class </em><tt class="descname">MarkovRateTable</tt><a class="headerlink" href="#MarkovRateTable" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="MarkovRateTable.channel">
-<tt class="descname">channel</tt><a class="headerlink" href="#MarkovRateTable.channel" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This message couples the rate table to the compartment. The rate table needs updates on voltage in order to compute the rate table.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovRateTable.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#MarkovRateTable.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.handleVm">
-<tt class="descname">handleVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.handleVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles incoming message containing voltage information.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.init">
-<tt class="descname">init</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.init" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Initialization of the class. Allocates memory for all the tables.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.handleLigandConc">
-<tt class="descname">handleLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.handleLigandConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles incoming message containing ligand concentration.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.set1d">
-<tt class="descname">set1d</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.set1d" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Setting up of 1D lookup table for the (i,j)’th rate.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.set2d">
-<tt class="descname">set2d</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.set2d" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Setting up of 2D lookup table for the (i,j)’th rate.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.setconst">
-<tt class="descname">setconst</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.setconst" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Setting a constant value for the (i,j)’th rate. Internally, this is stored as a 1-D rate with a lookup table containing 1 entry.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.setVm">
-<tt class="descname">setVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.setVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.getVm">
-<tt class="descname">getVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.getVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.setLigandConc">
-<tt class="descname">setLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.setLigandConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.getLigandConc">
-<tt class="descname">getLigandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.getLigandConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.getQ">
-<tt class="descname">getQ</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.getQ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovRateTable.getSize">
-<tt class="descname">getSize</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovRateTable.getSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovRateTable.instratesOut">
-<tt class="descname">instratesOut</tt><a class="headerlink" href="#MarkovRateTable.instratesOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector< vector<double> > (<em>source message field</em>) Sends out instantaneous rate information of varying transition ratesat each time step.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovRateTable.Vm">
-<tt class="descname">Vm</tt><a class="headerlink" href="#MarkovRateTable.Vm" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Membrane voltage.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovRateTable.ligandConc">
-<tt class="descname">ligandConc</tt><a class="headerlink" href="#MarkovRateTable.ligandConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Ligand concentration.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovRateTable.Q">
-<tt class="descname">Q</tt><a class="headerlink" href="#MarkovRateTable.Q" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector< vector<double> > (<em>value field</em>) Instantaneous rate matrix.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovRateTable.size">
-<tt class="descname">size</tt><a class="headerlink" href="#MarkovRateTable.size" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Dimension of the families of lookup tables. Is always equal to the number of states in the model.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="MarkovSolver">
-<em class="property">class </em><tt class="descname">MarkovSolver</tt><a class="headerlink" href="#MarkovSolver" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="MarkovSolver.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#MarkovSolver.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolver.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolver.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolver.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolver.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="MarkovSolverBase">
-<em class="property">class </em><tt class="descname">MarkovSolverBase</tt><a class="headerlink" href="#MarkovSolverBase" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="MarkovSolverBase.channel">
-<tt class="descname">channel</tt><a class="headerlink" href="#MarkovSolverBase.channel" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#MarkovSolverBase.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.handleVm">
-<tt class="descname">handleVm</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.handleVm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles incoming message containing voltage information.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.ligandConc">
-<tt class="descname">ligandConc</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.ligandConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles incoming message containing ligand concentration.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.init">
-<tt class="descname">init</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.init" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Setups the table of matrix exponentials associated with the solver object.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getQ">
-<tt class="descname">getQ</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getQ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getState">
-<tt class="descname">getState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getState" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.setInitialState">
-<tt class="descname">setInitialState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setInitialState" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getInitialState">
-<tt class="descname">getInitialState</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getInitialState" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.setXmin">
-<tt class="descname">setXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setXmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getXmin">
-<tt class="descname">getXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getXmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.setXmax">
-<tt class="descname">setXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setXmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getXmax">
-<tt class="descname">getXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getXmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.setXdivs">
-<tt class="descname">setXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setXdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getXdivs">
-<tt class="descname">getXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getXdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getInvdx">
-<tt class="descname">getInvdx</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getInvdx" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.setYmin">
-<tt class="descname">setYmin</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setYmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getYmin">
-<tt class="descname">getYmin</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getYmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.setYmax">
-<tt class="descname">setYmax</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setYmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getYmax">
-<tt class="descname">getYmax</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getYmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.setYdivs">
-<tt class="descname">setYdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.setYdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getYdivs">
-<tt class="descname">getYdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getYdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MarkovSolverBase.getInvdy">
-<tt class="descname">getInvdy</tt><big>(</big><big>)</big><a class="headerlink" href="#MarkovSolverBase.getInvdy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.stateOut">
-<tt class="descname">stateOut</tt><a class="headerlink" href="#MarkovSolverBase.stateOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>source message field</em>) Sends updated state to the MarkovChannel class.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.Q">
-<tt class="descname">Q</tt><a class="headerlink" href="#MarkovSolverBase.Q" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector< vector<double> > (<em>value field</em>) Instantaneous rate matrix.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.state">
-<tt class="descname">state</tt><a class="headerlink" href="#MarkovSolverBase.state" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Current state of the channel.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.initialState">
-<tt class="descname">initialState</tt><a class="headerlink" href="#MarkovSolverBase.initialState" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Initial state of the channel.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.xmin">
-<tt class="descname">xmin</tt><a class="headerlink" href="#MarkovSolverBase.xmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum value for x axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.xmax">
-<tt class="descname">xmax</tt><a class="headerlink" href="#MarkovSolverBase.xmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximum value for x axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.xdivs">
-<tt class="descname">xdivs</tt><a class="headerlink" href="#MarkovSolverBase.xdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) # of divisions on x axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.invdx">
-<tt class="descname">invdx</tt><a class="headerlink" href="#MarkovSolverBase.invdx" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Reciprocal of increment on x axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.ymin">
-<tt class="descname">ymin</tt><a class="headerlink" href="#MarkovSolverBase.ymin" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum value for y axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.ymax">
-<tt class="descname">ymax</tt><a class="headerlink" href="#MarkovSolverBase.ymax" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximum value for y axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.ydivs">
-<tt class="descname">ydivs</tt><a class="headerlink" href="#MarkovSolverBase.ydivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) # of divisions on y axis of lookup table</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MarkovSolverBase.invdy">
-<tt class="descname">invdy</tt><a class="headerlink" href="#MarkovSolverBase.invdy" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Reciprocal of increment on y axis of lookup table</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="MathFunc">
-<em class="property">class </em><tt class="descname">MathFunc</tt><a class="headerlink" href="#MathFunc" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="MathFunc.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#MathFunc.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.setMathML">
-<tt class="descname">setMathML</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.setMathML" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.getMathML">
-<tt class="descname">getMathML</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.getMathML" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.setFunction">
-<tt class="descname">setFunction</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.setFunction" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.getFunction">
-<tt class="descname">getFunction</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.getFunction" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.getResult">
-<tt class="descname">getResult</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.getResult" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.arg1">
-<tt class="descname">arg1</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.arg1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle arg1</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.arg2">
-<tt class="descname">arg2</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.arg2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle arg2</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.arg3">
-<tt class="descname">arg3</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.arg3" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle arg3</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.arg4">
-<tt class="descname">arg4</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.arg4" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle arg4</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MathFunc.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MathFunc.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MathFunc.output">
-<tt class="descname">output</tt><a class="headerlink" href="#MathFunc.output" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out result of computation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MathFunc.mathML">
-<tt class="descname">mathML</tt><a class="headerlink" href="#MathFunc.mathML" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) MathML version of expression to compute</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MathFunc.function">
-<tt class="descname">function</tt><a class="headerlink" href="#MathFunc.function" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) function is for functions of form f(x, y) = x + y</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MathFunc.result">
-<tt class="descname">result</tt><a class="headerlink" href="#MathFunc.result" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) result value</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="MeshEntry">
-<em class="property">class </em><tt class="descname">MeshEntry</tt><a class="headerlink" href="#MeshEntry" title="Permalink to this definition">¶</a></dt>
-<dd><p>One voxel in a chemical reaction compartment</p>
-<dl class="attribute">
-<dt id="MeshEntry.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#MeshEntry.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.mesh">
-<tt class="descname">mesh</tt><a class="headerlink" href="#MeshEntry.mesh" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for updating mesh volumes and subdivisions,typically controls pool volumes</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MeshEntry.getVolume">
-<tt class="descname">getVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MeshEntry.getDimensions">
-<tt class="descname">getDimensions</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getDimensions" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MeshEntry.getMeshType">
-<tt class="descname">getMeshType</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getMeshType" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MeshEntry.getCoordinates">
-<tt class="descname">getCoordinates</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getCoordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MeshEntry.getNeighbors">
-<tt class="descname">getNeighbors</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getNeighbors" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MeshEntry.getDiffusionArea">
-<tt class="descname">getDiffusionArea</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getDiffusionArea" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MeshEntry.getDiffusionScaling">
-<tt class="descname">getDiffusionScaling</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.getDiffusionScaling" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MeshEntry.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MeshEntry.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MeshEntry.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">getVolume</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.remeshOut">
-<tt class="descname">remeshOut</tt><a class="headerlink" href="#MeshEntry.remeshOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,unsigned int,unsigned int,vector<unsigned int>,vector<double> (<em>source message field</em>) Tells the target pool or other entity that the compartment subdivision(meshing) has changed, and that it has to redo its volume and memory allocation accordingly.Arguments are: oldvol, numTotalEntries, startEntry, localIndices, volsThe vols specifies volumes of each local mesh entry. It also specifieshow many meshEntries are present on the local node.The localIndices vector is used for general load balancing only.It has a list of the all meshEntries on current node.If it is empty, we assume block load balancing. In this secondcase the contents of the current node go from startEntry to startEntry + vols.size().</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.remeshReacsOut">
-<tt class="descname">remeshReacsOut</tt><a class="headerlink" href="#MeshEntry.remeshReacsOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>source message field</em>) Tells connected enz or reac that the compartment subdivision(meshing) has changed, and that it has to redo its volume-dependent rate terms like <a href="#id23"><span class="problematic" id="id24">numKf_</span></a> accordingly.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.volume">
-<tt class="descname">volume</tt><a class="headerlink" href="#MeshEntry.volume" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Volume of this MeshEntry</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.dimensions">
-<tt class="descname">dimensions</tt><a class="headerlink" href="#MeshEntry.dimensions" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) number of dimensions of this MeshEntry</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.meshType">
-<tt class="descname">meshType</tt><a class="headerlink" href="#MeshEntry.meshType" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder 3. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.Coordinates">
-<tt class="descname">Coordinates</tt><a class="headerlink" href="#MeshEntry.Coordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Coordinates that define current MeshEntry. Depend on MeshType.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.neighbors">
-<tt class="descname">neighbors</tt><a class="headerlink" href="#MeshEntry.neighbors" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int> (<em>value field</em>) Indices of other MeshEntries that this one connects to</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.DiffusionArea">
-<tt class="descname">DiffusionArea</tt><a class="headerlink" href="#MeshEntry.DiffusionArea" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Diffusion area for geometry of interface</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MeshEntry.DiffusionScaling">
-<tt class="descname">DiffusionScaling</tt><a class="headerlink" href="#MeshEntry.DiffusionScaling" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) Diffusion scaling for geometry of interface</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="MgBlock">
-<em class="property">class </em><tt class="descname">MgBlock</tt><a class="headerlink" href="#MgBlock" title="Permalink to this definition">¶</a></dt>
-<dd><blockquote>
-<div><p>MgBlock: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.</p>
-<dl class="attribute">
-<dt id="MgBlock.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#MgBlock.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</p>
-</dd></dl>
-
-</div></blockquote>
-<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-<blockquote>
-<div><dl class="method">
-<dt id="MgBlock.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.origChannel">
-<tt class="descname">origChannel</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.origChannel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.setKMg_A">
-<tt class="descname">setKMg_A</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setKMg_A" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.getKMg_A">
-<tt class="descname">getKMg_A</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getKMg_A" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.setKMg_B">
-<tt class="descname">setKMg_B</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setKMg_B" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.getKMg_B">
-<tt class="descname">getKMg_B</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getKMg_B" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.setCMg">
-<tt class="descname">setCMg</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setCMg" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.getCMg">
-<tt class="descname">getCMg</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getCMg" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.setIk">
-<tt class="descname">setIk</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setIk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.getIk">
-<tt class="descname">getIk</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getIk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.setZk">
-<tt class="descname">setZk</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.setZk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="MgBlock.getZk">
-<tt class="descname">getZk</tt><big>(</big><big>)</big><a class="headerlink" href="#MgBlock.getZk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MgBlock.KMg_A">
-<tt class="descname">KMg_A</tt><a class="headerlink" href="#MgBlock.KMg_A" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) 1/eta</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MgBlock.KMg_B">
-<tt class="descname">KMg_B</tt><a class="headerlink" href="#MgBlock.KMg_B" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) 1/gamma</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MgBlock.CMg">
-<tt class="descname">CMg</tt><a class="headerlink" href="#MgBlock.CMg" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) [Mg] in mM</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MgBlock.Ik">
-<tt class="descname">Ik</tt><a class="headerlink" href="#MgBlock.Ik" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Current through MgBlock</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="MgBlock.Zk">
-<tt class="descname">Zk</tt><a class="headerlink" href="#MgBlock.Zk" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Charge on ion</p>
-</dd></dl>
-
-</div></blockquote>
-</dd></dl>
-
-<dl class="class">
-<dt id="Msg">
-<em class="property">class </em><tt class="descname">Msg</tt><a class="headerlink" href="#Msg" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="Msg.getE1">
-<tt class="descname">getE1</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getE1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Msg.getE2">
-<tt class="descname">getE2</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getE2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Msg.getSrcFieldsOnE1">
-<tt class="descname">getSrcFieldsOnE1</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getSrcFieldsOnE1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Msg.getDestFieldsOnE2">
-<tt class="descname">getDestFieldsOnE2</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getDestFieldsOnE2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Msg.getSrcFieldsOnE2">
-<tt class="descname">getSrcFieldsOnE2</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getSrcFieldsOnE2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Msg.getDestFieldsOnE1">
-<tt class="descname">getDestFieldsOnE1</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getDestFieldsOnE1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Msg.getAdjacent">
-<tt class="descname">getAdjacent</tt><big>(</big><big>)</big><a class="headerlink" href="#Msg.getAdjacent" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Msg.e1">
-<tt class="descname">e1</tt><a class="headerlink" href="#Msg.e1" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Id of source Element.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Msg.e2">
-<tt class="descname">e2</tt><a class="headerlink" href="#Msg.e2" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Id of source Element.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Msg.srcFieldsOnE1">
-<tt class="descname">srcFieldsOnE1</tt><a class="headerlink" href="#Msg.srcFieldsOnE1" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Msg.destFieldsOnE2">
-<tt class="descname">destFieldsOnE2</tt><a class="headerlink" href="#Msg.destFieldsOnE2" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Msg.srcFieldsOnE2">
-<tt class="descname">srcFieldsOnE2</tt><a class="headerlink" href="#Msg.srcFieldsOnE2" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Msg.destFieldsOnE1">
-<tt class="descname">destFieldsOnE1</tt><a class="headerlink" href="#Msg.destFieldsOnE1" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Msg.adjacent">
-<tt class="descname">adjacent</tt><a class="headerlink" href="#Msg.adjacent" title="Permalink to this definition">¶</a></dt>
-<dd><p>ObjId,ObjId (<em>lookup field</em>) The element adjacent to the specified element</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Mstring">
-<em class="property">class </em><tt class="descname">Mstring</tt><a class="headerlink" href="#Mstring" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="Mstring.setThis">
-<tt class="descname">setThis</tt><big>(</big><big>)</big><a class="headerlink" href="#Mstring.setThis" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Mstring.getThis">
-<tt class="descname">getThis</tt><big>(</big><big>)</big><a class="headerlink" href="#Mstring.getThis" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Mstring.setValue">
-<tt class="descname">setValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Mstring.setValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Mstring.getValue">
-<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Mstring.getValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Mstring.this">
-<tt class="descname">this</tt><a class="headerlink" href="#Mstring.this" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Access function for entire Mstring object.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Mstring.value">
-<tt class="descname">value</tt><a class="headerlink" href="#Mstring.value" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Access function for value field of Mstring object,which happens also to be the entire contents of the object.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Nernst">
-<em class="property">class </em><tt class="descname">Nernst</tt><a class="headerlink" href="#Nernst" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="Nernst.getE">
-<tt class="descname">getE</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getE" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.setTemperature">
-<tt class="descname">setTemperature</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.getTemperature">
-<tt class="descname">getTemperature</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.setValence">
-<tt class="descname">setValence</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setValence" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.getValence">
-<tt class="descname">getValence</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getValence" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.setCin">
-<tt class="descname">setCin</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setCin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.getCin">
-<tt class="descname">getCin</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getCin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.setCout">
-<tt class="descname">setCout</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setCout" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.getCout">
-<tt class="descname">getCout</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getCout" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.setScale">
-<tt class="descname">setScale</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.setScale" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.getScale">
-<tt class="descname">getScale</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.getScale" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.ci">
-<tt class="descname">ci</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.ci" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Set internal conc of ion, and immediately send out the updated E</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Nernst.co">
-<tt class="descname">co</tt><big>(</big><big>)</big><a class="headerlink" href="#Nernst.co" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Set external conc of ion, and immediately send out the updated E</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Nernst.Eout">
-<tt class="descname">Eout</tt><a class="headerlink" href="#Nernst.Eout" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Computed reversal potential</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Nernst.E">
-<tt class="descname">E</tt><a class="headerlink" href="#Nernst.E" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Computed reversal potential</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Nernst.Temperature">
-<tt class="descname">Temperature</tt><a class="headerlink" href="#Nernst.Temperature" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Temperature of cell</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Nernst.valence">
-<tt class="descname">valence</tt><a class="headerlink" href="#Nernst.valence" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) Valence of ion in Nernst calculation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Nernst.Cin">
-<tt class="descname">Cin</tt><a class="headerlink" href="#Nernst.Cin" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Internal conc of ion</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Nernst.Cout">
-<tt class="descname">Cout</tt><a class="headerlink" href="#Nernst.Cout" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) External conc of ion</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Nernst.scale">
-<tt class="descname">scale</tt><a class="headerlink" href="#Nernst.scale" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Voltage scale factor</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="NeuroMesh">
-<em class="property">class </em><tt class="descname">NeuroMesh</tt><a class="headerlink" href="#NeuroMesh" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="NeuroMesh.setCell">
-<tt class="descname">setCell</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setCell" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.getCell">
-<tt class="descname">getCell</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getCell" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.setSubTree">
-<tt class="descname">setSubTree</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setSubTree" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.getSubTree">
-<tt class="descname">getSubTree</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getSubTree" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.setSeparateSpines">
-<tt class="descname">setSeparateSpines</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setSeparateSpines" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.getSeparateSpines">
-<tt class="descname">getSeparateSpines</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getSeparateSpines" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.getNumSegments">
-<tt class="descname">getNumSegments</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getNumSegments" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.getNumDiffCompts">
-<tt class="descname">getNumDiffCompts</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getNumDiffCompts" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.getParentVoxel">
-<tt class="descname">getParentVoxel</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getParentVoxel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.setDiffLength">
-<tt class="descname">setDiffLength</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setDiffLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.getDiffLength">
-<tt class="descname">getDiffLength</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getDiffLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.setGeometryPolicy">
-<tt class="descname">setGeometryPolicy</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.setGeometryPolicy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.getGeometryPolicy">
-<tt class="descname">getGeometryPolicy</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.getGeometryPolicy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="NeuroMesh.cellPortion">
-<tt class="descname">cellPortion</tt><big>(</big><big>)</big><a class="headerlink" href="#NeuroMesh.cellPortion" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Tells NeuroMesh to mesh up a subpart of a cell. For nowassumed contiguous.The first argument is the cell Id. The second is the wildcardpath of compartments to use for the subpart.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.spineListOut">
-<tt class="descname">spineListOut</tt><a class="headerlink" href="#NeuroMesh.spineListOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id,vector<Id>,vector<Id>,vector<unsigned int> (<em>source message field</em>) Request SpineMesh to construct self based on list of electrical compartments that this NeuroMesh has determined are spine shaft and spine head respectively. Also passes in the info about where each spine is connected to the NeuroMesh. Arguments: Cell Id, shaft compartment Ids, head compartment Ids,index of matching parent voxels for each spine</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.psdListOut">
-<tt class="descname">psdListOut</tt><a class="headerlink" href="#NeuroMesh.psdListOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id,vector<double>,vector<unsigned int> (<em>source message field</em>) Tells PsdMesh to build a mesh. Arguments: Cell Id, Coordinates of each psd, index of matching parent voxels for each spineThe coordinates each have 8 entries:xyz of centre of psd, xyz of vector perpendicular to psd, psd diameter, diffusion distance from parent compartment to PSD</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.cell">
-<tt class="descname">cell</tt><a class="headerlink" href="#NeuroMesh.cell" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Id for base element of cell model. Uses this to traverse theentire tree of the cell to build the mesh.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.subTree">
-<tt class="descname">subTree</tt><a class="headerlink" href="#NeuroMesh.subTree" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<Id> (<em>value field</em>) Set of compartments to model. If they happen to be contiguousthen also set up diffusion between the compartments. Can alsohandle cases where the same cell is divided into multiplenon-diffusively-coupled compartments</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.separateSpines">
-<tt class="descname">separateSpines</tt><a class="headerlink" href="#NeuroMesh.separateSpines" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Flag: when separateSpines is true, the traversal separates any compartment with the strings ‘spine’, ‘head’, ‘shaft’ or ‘neck’ in its name,Allows to set up separate mesh for spines, based on the same cell model. Requires for the spineListOut message tobe sent to the target SpineMesh object.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.numSegments">
-<tt class="descname">numSegments</tt><a class="headerlink" href="#NeuroMesh.numSegments" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of cylindrical/spherical segments in model</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.numDiffCompts">
-<tt class="descname">numDiffCompts</tt><a class="headerlink" href="#NeuroMesh.numDiffCompts" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of diffusive compartments in model</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.parentVoxel">
-<tt class="descname">parentVoxel</tt><a class="headerlink" href="#NeuroMesh.parentVoxel" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int> (<em>value field</em>) Vector of indices of parents of each voxel.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.diffLength">
-<tt class="descname">diffLength</tt><a class="headerlink" href="#NeuroMesh.diffLength" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Diffusive length constant to use for subdivisions. The system willattempt to subdivide cell using diffusive compartments ofthe specified diffusion lengths as a maximum.In order to get integral numbersof compartments in each segment, it may subdivide more finely.Uses default of 0.5 microns, that is, half typical lambda.For default, consider a tau of about 1 second for mostreactions, and a diffusion const of about 1e-12 um^2/sec.This gives lambda of 1 micron</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="NeuroMesh.geometryPolicy">
-<tt class="descname">geometryPolicy</tt><a class="headerlink" href="#NeuroMesh.geometryPolicy" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Policy for how to interpret electrical model geometry (which is a branching 1-dimensional tree) in terms of 3-D constructslike spheres, cylinders, and cones.There are three options, default, trousers, and cylinder:default mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites and dendrites emerging from soma, proximal diameter is from compt dia. Don’t worry about overlap. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.trousers mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites, use a trouser function. Avoid overlap. - For soma, use some variant of trousers. Here we must avoid overlap - For spines, use a way to smoothly merge into parent dend. Radius of curvature should be similar to that of the spine neck. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.cylinder mode: - Use cylinders. Diameter is just compartment dia. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle. - Ignore spatial overlap.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Neuron">
-<em class="property">class </em><tt class="descname">Neuron</tt><a class="headerlink" href="#Neuron" title="Permalink to this definition">¶</a></dt>
-<dd><p>Neuron - A compartment container</p>
-</dd></dl>
-
-<dl class="class">
-<dt id="Neutral">
-<em class="property">class </em><tt class="descname">Neutral</tt><a class="headerlink" href="#Neutral" title="Permalink to this definition">¶</a></dt>
-<dd><p>Neutral: Base class for all MOOSE classes. Providesaccess functions for housekeeping fields and operations, messagetraversal, and so on.</p>
-<dl class="method">
-<dt id="Neutral.parentMsg">
-<tt class="descname">parentMsg</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.parentMsg" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Message from Parent Element(s)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.setThis">
-<tt class="descname">setThis</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.setThis" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getThis">
-<tt class="descname">getThis</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getThis" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.setName">
-<tt class="descname">setName</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.setName" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getName">
-<tt class="descname">getName</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getName" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getMe">
-<tt class="descname">getMe</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMe" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getParent">
-<tt class="descname">getParent</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getParent" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getChildren">
-<tt class="descname">getChildren</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getChildren" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getPath">
-<tt class="descname">getPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getPath" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getClassName">
-<tt class="descname">getClassName</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getClassName" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.setNumData">
-<tt class="descname">setNumData</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.setNumData" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getNumData">
-<tt class="descname">getNumData</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getNumData" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.setNumField">
-<tt class="descname">setNumField</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.setNumField" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getNumField">
-<tt class="descname">getNumField</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getNumField" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getValueFields">
-<tt class="descname">getValueFields</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getValueFields" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getSourceFields">
-<tt class="descname">getSourceFields</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getSourceFields" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getDestFields">
-<tt class="descname">getDestFields</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getDestFields" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getMsgOut">
-<tt class="descname">getMsgOut</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMsgOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getMsgIn">
-<tt class="descname">getMsgIn</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMsgIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getNeighbors">
-<tt class="descname">getNeighbors</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getNeighbors" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getMsgDests">
-<tt class="descname">getMsgDests</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMsgDests" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Neutral.getMsgDestFunctions">
-<tt class="descname">getMsgDestFunctions</tt><big>(</big><big>)</big><a class="headerlink" href="#Neutral.getMsgDestFunctions" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.childOut">
-<tt class="descname">childOut</tt><a class="headerlink" href="#Neutral.childOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>source message field</em>) Message to child Elements</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.this">
-<tt class="descname">this</tt><a class="headerlink" href="#Neutral.this" title="Permalink to this definition">¶</a></dt>
-<dd><p>Neutral (<em>value field</em>) Access function for entire object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.name">
-<tt class="descname">name</tt><a class="headerlink" href="#Neutral.name" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Name of object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.me">
-<tt class="descname">me</tt><a class="headerlink" href="#Neutral.me" title="Permalink to this definition">¶</a></dt>
-<dd><p>ObjId (<em>value field</em>) ObjId for current object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.parent">
-<tt class="descname">parent</tt><a class="headerlink" href="#Neutral.parent" title="Permalink to this definition">¶</a></dt>
-<dd><p>ObjId (<em>value field</em>) Parent ObjId for current object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.children">
-<tt class="descname">children</tt><a class="headerlink" href="#Neutral.children" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<Id> (<em>value field</em>) vector of ObjIds listing all children of current object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.path">
-<tt class="descname">path</tt><a class="headerlink" href="#Neutral.path" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) text path for object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.className">
-<tt class="descname">className</tt><a class="headerlink" href="#Neutral.className" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Class Name of object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.numData">
-<tt class="descname">numData</tt><a class="headerlink" href="#Neutral.numData" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) # of Data entries on Element.Note that on a FieldElement this does NOT refer to field entries,but to the number of DataEntries on the parent of the FieldElement.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.numField">
-<tt class="descname">numField</tt><a class="headerlink" href="#Neutral.numField" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) For a FieldElement: number of entries of self.For a regular Element: One.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.valueFields">
-<tt class="descname">valueFields</tt><a class="headerlink" href="#Neutral.valueFields" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) List of all value fields on Element.These fields are accessed through the assignment operations in the Python interface.These fields may also be accessed as functions through the set<FieldName> and get<FieldName> commands.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.sourceFields">
-<tt class="descname">sourceFields</tt><a class="headerlink" href="#Neutral.sourceFields" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) List of all source fields on Element, that is fields that can act as message sources.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.destFields">
-<tt class="descname">destFields</tt><a class="headerlink" href="#Neutral.destFields" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<string> (<em>value field</em>) List of all destination fields on Element, that is, fieldsthat are accessed as Element functions.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.msgOut">
-<tt class="descname">msgOut</tt><a class="headerlink" href="#Neutral.msgOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<ObjId> (<em>value field</em>) Messages going out from this Element</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.msgIn">
-<tt class="descname">msgIn</tt><a class="headerlink" href="#Neutral.msgIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<ObjId> (<em>value field</em>) Messages coming in to this Element</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.neighbors">
-<tt class="descname">neighbors</tt><a class="headerlink" href="#Neutral.neighbors" title="Permalink to this definition">¶</a></dt>
-<dd><p>string,vector<Id> (<em>lookup field</em>) Ids of Elements connected this Element on specified field.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.msgDests">
-<tt class="descname">msgDests</tt><a class="headerlink" href="#Neutral.msgDests" title="Permalink to this definition">¶</a></dt>
-<dd><p>string,vector<ObjId> (<em>lookup field</em>) ObjIds receiving messages from the specified SrcFinfo</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Neutral.msgDestFunctions">
-<tt class="descname">msgDestFunctions</tt><a class="headerlink" href="#Neutral.msgDestFunctions" title="Permalink to this definition">¶</a></dt>
-<dd><p>string,vector<string> (<em>lookup field</em>) Matching function names for each ObjId receiving a msg from the specified SrcFinfo</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="OneToAllMsg">
-<em class="property">class </em><tt class="descname">OneToAllMsg</tt><a class="headerlink" href="#OneToAllMsg" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="OneToAllMsg.setI1">
-<tt class="descname">setI1</tt><big>(</big><big>)</big><a class="headerlink" href="#OneToAllMsg.setI1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="OneToAllMsg.getI1">
-<tt class="descname">getI1</tt><big>(</big><big>)</big><a class="headerlink" href="#OneToAllMsg.getI1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="OneToAllMsg.i1">
-<tt class="descname">i1</tt><a class="headerlink" href="#OneToAllMsg.i1" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) DataId of source Element.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="OneToOneDataIndexMsg">
-<em class="property">class </em><tt class="descname">OneToOneDataIndexMsg</tt><a class="headerlink" href="#OneToOneDataIndexMsg" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="OneToOneMsg">
-<em class="property">class </em><tt class="descname">OneToOneMsg</tt><a class="headerlink" href="#OneToOneMsg" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="PIDController">
-<em class="property">class </em><tt class="descname">PIDController</tt><a class="headerlink" href="#PIDController" title="Permalink to this definition">¶</a></dt>
-<dd><p>PID feedback controller.PID stands for Proportional-Integral-Derivative. It is used to feedback control dynamical systems. It tries to create a feedback output such that the sensed (measured) parameter is held at command value. Refer to wikipedia (<a class="reference external" href="http://wikipedia.org">http://wikipedia.org</a>) for details on PID Controller.</p>
-<dl class="attribute">
-<dt id="PIDController.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#PIDController.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.setGain">
-<tt class="descname">setGain</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setGain" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getGain">
-<tt class="descname">getGain</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getGain" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.setSaturation">
-<tt class="descname">setSaturation</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setSaturation" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getSaturation">
-<tt class="descname">getSaturation</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getSaturation" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.setCommand">
-<tt class="descname">setCommand</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setCommand" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getCommand">
-<tt class="descname">getCommand</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getCommand" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getSensed">
-<tt class="descname">getSensed</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getSensed" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.setTauI">
-<tt class="descname">setTauI</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setTauI" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getTauI">
-<tt class="descname">getTauI</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getTauI" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.setTauD">
-<tt class="descname">setTauD</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.setTauD" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getTauD">
-<tt class="descname">getTauD</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getTauD" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getOutputValue">
-<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getOutputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getError">
-<tt class="descname">getError</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getError" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getIntegral">
-<tt class="descname">getIntegral</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getIntegral" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getDerivative">
-<tt class="descname">getDerivative</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getDerivative" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.getE_previous">
-<tt class="descname">getE_previous</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.getE_previous" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.commandIn">
-<tt class="descname">commandIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.commandIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Command (desired value) input. This is known as setpoint (SP) in control theory.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.sensedIn">
-<tt class="descname">sensedIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.sensedIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Sensed parameter - this is the one to be tuned. This is known as process variable (PV) in control theory. This comes from the process we are trying to control.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.gainDest">
-<tt class="descname">gainDest</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.gainDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Destination message to control the PIDController gain dynamically.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle process calls.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PIDController.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#PIDController.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Reinitialize the object.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PIDController.output">
-<tt class="descname">output</tt><a class="headerlink" href="#PIDController.output" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends the output of the PIDController. This is known as manipulated variable (MV) in control theory. This should be fed into the process which we are trying to control.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PIDController.gain">
-<tt class="descname">gain</tt><a class="headerlink" href="#PIDController.gain" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) This is the proportional gain (Kp). This tuning parameter scales the proportional term. Larger gain usually results in faster response, but too much will lead to instability and oscillation.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PIDController.saturation">
-<tt class="descname">saturation</tt><a class="headerlink" href="#PIDController.saturation" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Bound on the permissible range of output. Defaults to maximum double value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PIDController.command">
-<tt class="descname">command</tt><a class="headerlink" href="#PIDController.command" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) The command (desired) value of the sensed parameter. In control theory this is commonly known as setpoint(SP).</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PIDController.sensed">
-<tt class="descname">sensed</tt><a class="headerlink" href="#PIDController.sensed" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Sensed (measured) value. This is commonly known as process variable(PV) in control theory.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PIDController.tauI">
-<tt class="descname">tauI</tt><a class="headerlink" href="#PIDController.tauI" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) The integration time constant, typically = dt. This is actually proportional gain divided by integral gain (Kp/Ki)). Larger Ki (smaller tauI) usually leads to fast elimination of steady state errors at the cost of larger overshoot.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PIDController.tauD">
-<tt class="descname">tauD</tt><a class="headerlink" href="#PIDController.tauD" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) The differentiation time constant, typically = dt / 4. This is derivative gain (Kd) times proportional gain (Kp). Larger Kd (tauD) decreases overshoot at the cost of slowing down transient response and may lead to instability.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PIDController.outputValue">
-<tt class="descname">outputValue</tt><a class="headerlink" href="#PIDController.outputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Output of the PIDController. This is given by: gain * ( error + INTEGRAL[ error dt ] / tau_i + tau_d * d(error)/dt )</p>
-</dd></dl>
-
-</dd></dl>
-
-<p>Where gain = proportional gain (Kp), tau_i = integral gain (Kp/Ki) and tau_d = derivative gain (Kd/Kp). In control theory this is also known as the manipulated variable (MV)</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="error">
-<tt class="descname">error</tt><a class="headerlink" href="#error" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) The error term, which is the difference between command and sensed value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="integral">
-<tt class="descname">integral</tt><a class="headerlink" href="#integral" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) The integral term. It is calculated as INTEGRAL(error dt) = previous_integral + dt * (error + e_previous)/2.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt>
-<tt class="descname">derivative</tt></dt>
-<dd><p>double (<em>value field</em>) The derivative term. This is (error - e_previous)/dt.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="e_previous">
-<tt class="descname">e_previous</tt><a class="headerlink" href="#e_previous" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) The error term for previous step.</p>
-</dd></dl>
-
-</div></blockquote>
-<dl class="class">
-<dt id="Pool">
-<em class="property">class </em><tt class="descname">Pool</tt><a class="headerlink" href="#Pool" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="Pool.increment">
-<tt class="descname">increment</tt><big>(</big><big>)</big><a class="headerlink" href="#Pool.increment" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Increments mol numbers by specified amount. Can be +ve or -ve</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Pool.decrement">
-<tt class="descname">decrement</tt><big>(</big><big>)</big><a class="headerlink" href="#Pool.decrement" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Decrements mol numbers by specified amount. Can be +ve or -ve</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="PoolBase">
-<em class="property">class </em><tt class="descname">PoolBase</tt><a class="headerlink" href="#PoolBase" title="Permalink to this definition">¶</a></dt>
-<dd><p>Abstract base class for pools.</p>
-<dl class="attribute">
-<dt id="PoolBase.reac">
-<tt class="descname">reac</tt><a class="headerlink" href="#PoolBase.reac" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Connects to reaction</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#PoolBase.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.species">
-<tt class="descname">species</tt><a class="headerlink" href="#PoolBase.species" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for connecting to species objects</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.setN">
-<tt class="descname">setN</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setN" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.getN">
-<tt class="descname">getN</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getN" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.setNInit">
-<tt class="descname">setNInit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setNInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.getNInit">
-<tt class="descname">getNInit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getNInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.setDiffConst">
-<tt class="descname">setDiffConst</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setDiffConst" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.getDiffConst">
-<tt class="descname">getDiffConst</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getDiffConst" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.setMotorConst">
-<tt class="descname">setMotorConst</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setMotorConst" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.getMotorConst">
-<tt class="descname">getMotorConst</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getMotorConst" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.setConc">
-<tt class="descname">setConc</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.getConc">
-<tt class="descname">getConc</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getConc" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.setConcInit">
-<tt class="descname">setConcInit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setConcInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.getConcInit">
-<tt class="descname">getConcInit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getConcInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.setVolume">
-<tt class="descname">setVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.getVolume">
-<tt class="descname">getVolume</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getVolume" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.setSpeciesId">
-<tt class="descname">setSpeciesId</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.setSpeciesId" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.getSpeciesId">
-<tt class="descname">getSpeciesId</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.getSpeciesId" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.reacDest">
-<tt class="descname">reacDest</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.reacDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reaction input</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PoolBase.handleMolWt">
-<tt class="descname">handleMolWt</tt><big>(</big><big>)</big><a class="headerlink" href="#PoolBase.handleMolWt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.nOut">
-<tt class="descname">nOut</tt><a class="headerlink" href="#PoolBase.nOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out # of molecules in pool on each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.requestMolWt">
-<tt class="descname">requestMolWt</tt><a class="headerlink" href="#PoolBase.requestMolWt" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>source message field</em>) Requests Species object for mol wt</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.n">
-<tt class="descname">n</tt><a class="headerlink" href="#PoolBase.n" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Number of molecules in pool</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.nInit">
-<tt class="descname">nInit</tt><a class="headerlink" href="#PoolBase.nInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Initial value of number of molecules in pool</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.diffConst">
-<tt class="descname">diffConst</tt><a class="headerlink" href="#PoolBase.diffConst" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Diffusion constant of molecule</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.motorConst">
-<tt class="descname">motorConst</tt><a class="headerlink" href="#PoolBase.motorConst" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Motor transport rate molecule. + is away from soma, - is towards soma. Only relevant for ZombiePool subclasses.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.conc">
-<tt class="descname">conc</tt><a class="headerlink" href="#PoolBase.conc" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Concentration of molecules in this pool</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.concInit">
-<tt class="descname">concInit</tt><a class="headerlink" href="#PoolBase.concInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Initial value of molecular concentration in pool</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.volume">
-<tt class="descname">volume</tt><a class="headerlink" href="#PoolBase.volume" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Volume of compartment. Units are SI. Utility field, the actual volume info is stored on a volume mesh entry in the parent compartment.This mapping is implicit: the parent compartment must be somewhere up the element tree, and must have matching mesh entries. If the compartment isn’tavailable the volume is just taken as 1</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PoolBase.speciesId">
-<tt class="descname">speciesId</tt><a class="headerlink" href="#PoolBase.speciesId" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Species identifier for this mol pool. Eventually link to ontology.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="PostMaster">
-<em class="property">class </em><tt class="descname">PostMaster</tt><a class="headerlink" href="#PostMaster" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="PostMaster.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#PostMaster.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PostMaster.getNumNodes">
-<tt class="descname">getNumNodes</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.getNumNodes" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PostMaster.getMyNode">
-<tt class="descname">getMyNode</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.getMyNode" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PostMaster.setBufferSize">
-<tt class="descname">setBufferSize</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.setBufferSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PostMaster.getBufferSize">
-<tt class="descname">getBufferSize</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.getBufferSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PostMaster.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PostMaster.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#PostMaster.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PostMaster.numNodes">
-<tt class="descname">numNodes</tt><a class="headerlink" href="#PostMaster.numNodes" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Returns number of nodes that simulation runs on.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PostMaster.myNode">
-<tt class="descname">myNode</tt><a class="headerlink" href="#PostMaster.myNode" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Returns index of current node.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PostMaster.bufferSize">
-<tt class="descname">bufferSize</tt><a class="headerlink" href="#PostMaster.bufferSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Size of the send a receive buffers for each node.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="PsdMesh">
-<em class="property">class </em><tt class="descname">PsdMesh</tt><a class="headerlink" href="#PsdMesh" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="PsdMesh.setThickness">
-<tt class="descname">setThickness</tt><big>(</big><big>)</big><a class="headerlink" href="#PsdMesh.setThickness" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PsdMesh.getThickness">
-<tt class="descname">getThickness</tt><big>(</big><big>)</big><a class="headerlink" href="#PsdMesh.getThickness" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PsdMesh.psdList">
-<tt class="descname">psdList</tt><big>(</big><big>)</big><a class="headerlink" href="#PsdMesh.psdList" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Specifies the geometry of the spine,and the associated parent voxelArguments: cell container, disk params vector with 8 entriesper psd, parent voxel index</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PsdMesh.thickness">
-<tt class="descname">thickness</tt><a class="headerlink" href="#PsdMesh.thickness" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) An assumed thickness for PSD. The volume is computed as thePSD area passed in to each PSD, times this value.defaults to 50 nanometres. For reference, membranes are 5 nm.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="PulseGen">
-<em class="property">class </em><tt class="descname">PulseGen</tt><a class="headerlink" href="#PulseGen" title="Permalink to this definition">¶</a></dt>
-<dd><blockquote>
-<div><p>PulseGen: general purpose pulse generator. This can generate any number of pulses with specified level and duration.</p>
-<dl class="attribute">
-<dt id="PulseGen.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#PulseGen.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getOutputValue">
-<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getOutputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setBaseLevel">
-<tt class="descname">setBaseLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setBaseLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getBaseLevel">
-<tt class="descname">getBaseLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getBaseLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setFirstLevel">
-<tt class="descname">setFirstLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setFirstLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getFirstLevel">
-<tt class="descname">getFirstLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getFirstLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setFirstWidth">
-<tt class="descname">setFirstWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setFirstWidth" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getFirstWidth">
-<tt class="descname">getFirstWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getFirstWidth" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setFirstDelay">
-<tt class="descname">setFirstDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setFirstDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getFirstDelay">
-<tt class="descname">getFirstDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getFirstDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setSecondLevel">
-<tt class="descname">setSecondLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setSecondLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getSecondLevel">
-<tt class="descname">getSecondLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getSecondLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setSecondWidth">
-<tt class="descname">setSecondWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setSecondWidth" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getSecondWidth">
-<tt class="descname">getSecondWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getSecondWidth" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setSecondDelay">
-<tt class="descname">setSecondDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setSecondDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getSecondDelay">
-<tt class="descname">getSecondDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getSecondDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setCount">
-<tt class="descname">setCount</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setCount" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getCount">
-<tt class="descname">getCount</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getCount" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setTrigMode">
-<tt class="descname">setTrigMode</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setTrigMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getTrigMode">
-<tt class="descname">getTrigMode</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getTrigMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setLevel">
-<tt class="descname">setLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getLevel">
-<tt class="descname">getLevel</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setWidth">
-<tt class="descname">setWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setWidth" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getWidth">
-<tt class="descname">getWidth</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getWidth" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.setDelay">
-<tt class="descname">setDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.setDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.getDelay">
-<tt class="descname">getDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.getDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.input">
-<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.input" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle incoming input that determines gating/triggering onset.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.levelIn">
-<tt class="descname">levelIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.levelIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle level value coming from other objects</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.widthIn">
-<tt class="descname">widthIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.widthIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle width value coming from other objects</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.delayIn">
-<tt class="descname">delayIn</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.delayIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle delay value coming from other objects</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="PulseGen.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#PulseGen.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.output">
-<tt class="descname">output</tt><a class="headerlink" href="#PulseGen.output" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Current output level.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.outputValue">
-<tt class="descname">outputValue</tt><a class="headerlink" href="#PulseGen.outputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Output amplitude</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.baseLevel">
-<tt class="descname">baseLevel</tt><a class="headerlink" href="#PulseGen.baseLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Basal level of the stimulus</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.firstLevel">
-<tt class="descname">firstLevel</tt><a class="headerlink" href="#PulseGen.firstLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Amplitude of the first pulse in a sequence</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.firstWidth">
-<tt class="descname">firstWidth</tt><a class="headerlink" href="#PulseGen.firstWidth" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Width of the first pulse in a sequence</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.firstDelay">
-<tt class="descname">firstDelay</tt><a class="headerlink" href="#PulseGen.firstDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Delay to start of the first pulse in a sequence</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.secondLevel">
-<tt class="descname">secondLevel</tt><a class="headerlink" href="#PulseGen.secondLevel" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Amplitude of the second pulse in a sequence</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.secondWidth">
-<tt class="descname">secondWidth</tt><a class="headerlink" href="#PulseGen.secondWidth" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Width of the second pulse in a sequence</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.secondDelay">
-<tt class="descname">secondDelay</tt><a class="headerlink" href="#PulseGen.secondDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Delay to start of of the second pulse in a sequence</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.count">
-<tt class="descname">count</tt><a class="headerlink" href="#PulseGen.count" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of pulses in a sequence</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.trigMode">
-<tt class="descname">trigMode</tt><a class="headerlink" href="#PulseGen.trigMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Trigger mode for pulses in the sequence.</p>
-</dd></dl>
-
-</div></blockquote>
-<p>0 : free-running mode where it keeps looping its output
-1 : external trigger, where it is triggered by an external input (and stops after creating the first train of pulses)
-2 : external gate mode, where it keeps generating the pulses in a loop as long as the input is high.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="PulseGen.level">
-<tt class="descname">level</tt><a class="headerlink" href="#PulseGen.level" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Level of the pulse at specified index</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.width">
-<tt class="descname">width</tt><a class="headerlink" href="#PulseGen.width" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Width of the pulse at specified index</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="PulseGen.delay">
-<tt class="descname">delay</tt><a class="headerlink" href="#PulseGen.delay" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Delay of the pulse at specified index</p>
-</dd></dl>
-
-</div></blockquote>
-</dd></dl>
-
-<dl class="class">
-<dt id="RC">
-<em class="property">class </em><tt class="descname">RC</tt><a class="headerlink" href="#RC" title="Permalink to this definition">¶</a></dt>
-<dd><p>RC circuit: a series resistance R shunted by a capacitance C.</p>
-<dl class="attribute">
-<dt id="RC.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#RC.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.setV0">
-<tt class="descname">setV0</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.setV0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.getV0">
-<tt class="descname">getV0</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getV0" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.setR">
-<tt class="descname">setR</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.setR" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.getR">
-<tt class="descname">getR</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getR" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.setC">
-<tt class="descname">setC</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.setC" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.getC">
-<tt class="descname">getC</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getC" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.getState">
-<tt class="descname">getState</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getState" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.setInject">
-<tt class="descname">setInject</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.setInject" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.getInject">
-<tt class="descname">getInject</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.getInject" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.injectIn">
-<tt class="descname">injectIn</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.injectIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Receives input to the RC circuit. All incoming messages are summed up to give the total input current.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="RC.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#RC.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle reinitialization</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="RC.output">
-<tt class="descname">output</tt><a class="headerlink" href="#RC.output" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Current output level.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="RC.V0">
-<tt class="descname">V0</tt><a class="headerlink" href="#RC.V0" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Initial value of ‘state’</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="RC.R">
-<tt class="descname">R</tt><a class="headerlink" href="#RC.R" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Series resistance of the RC circuit.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="RC.C">
-<tt class="descname">C</tt><a class="headerlink" href="#RC.C" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Parallel capacitance of the RC circuit.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="RC.state">
-<tt class="descname">state</tt><a class="headerlink" href="#RC.state" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Output value of the RC circuit. This is the voltage across the capacitor.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="RC.inject">
-<tt class="descname">inject</tt><a class="headerlink" href="#RC.inject" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Input value to the RC circuit.This is handled as an input current to the circuit.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Reac">
-<em class="property">class </em><tt class="descname">Reac</tt><a class="headerlink" href="#Reac" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="ReacBase">
-<em class="property">class </em><tt class="descname">ReacBase</tt><a class="headerlink" href="#ReacBase" title="Permalink to this definition">¶</a></dt>
-<dd><p>Base class for reactions. Provides the MOOSE APIfunctions, but ruthlessly refers almost all of them to derivedclasses, which have to provide the man page output.</p>
-<dl class="attribute">
-<dt id="ReacBase.sub">
-<tt class="descname">sub</tt><a class="headerlink" href="#ReacBase.sub" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Connects to substrate pool</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.prd">
-<tt class="descname">prd</tt><a class="headerlink" href="#ReacBase.prd" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Connects to substrate pool</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#ReacBase.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.setNumKf">
-<tt class="descname">setNumKf</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.setNumKf" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.getNumKf">
-<tt class="descname">getNumKf</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getNumKf" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.setNumKb">
-<tt class="descname">setNumKb</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.setNumKb" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.getNumKb">
-<tt class="descname">getNumKb</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getNumKb" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.setKf">
-<tt class="descname">setKf</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.setKf" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.getKf">
-<tt class="descname">getKf</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getKf" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.setKb">
-<tt class="descname">setKb</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.setKb" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.getKb">
-<tt class="descname">getKb</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getKb" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.getNumSubstrates">
-<tt class="descname">getNumSubstrates</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getNumSubstrates" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.getNumProducts">
-<tt class="descname">getNumProducts</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.getNumProducts" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.subDest">
-<tt class="descname">subDest</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.subDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles # of molecules of substrate</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.prdDest">
-<tt class="descname">prdDest</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.prdDest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles # of molecules of product</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ReacBase.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#ReacBase.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.subOut">
-<tt class="descname">subOut</tt><a class="headerlink" href="#ReacBase.subOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.prdOut">
-<tt class="descname">prdOut</tt><a class="headerlink" href="#ReacBase.prdOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out increment of molecules on product each timestep</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.numKf">
-<tt class="descname">numKf</tt><a class="headerlink" href="#ReacBase.numKf" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Forward rate constant, in # units</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.numKb">
-<tt class="descname">numKb</tt><a class="headerlink" href="#ReacBase.numKb" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Reverse rate constant, in # units</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.Kf">
-<tt class="descname">Kf</tt><a class="headerlink" href="#ReacBase.Kf" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Forward rate constant, in concentration units</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.Kb">
-<tt class="descname">Kb</tt><a class="headerlink" href="#ReacBase.Kb" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Reverse rate constant, in concentration units</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.numSubstrates">
-<tt class="descname">numSubstrates</tt><a class="headerlink" href="#ReacBase.numSubstrates" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of substrates of reaction</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ReacBase.numProducts">
-<tt class="descname">numProducts</tt><a class="headerlink" href="#ReacBase.numProducts" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of products of reaction</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Shell">
-<em class="property">class </em><tt class="descname">Shell</tt><a class="headerlink" href="#Shell" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="Shell.setclock">
-<tt class="descname">setclock</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.setclock" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns clock ticks. Args: tick#, dt</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Shell.create">
-<tt class="descname">create</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.create" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) create( class, parent, newElm, name, numData, isGlobal )</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Shell.delete">
-<tt class="descname">delete</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.delete" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Destroys Element, all its messages, and all its children. Args: Id</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Shell.copy">
-<tt class="descname">copy</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.copy" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): The vector< Id > has Id orig, Id newParent, Id newElm. This function copies an Element and all its children to a new parent. May also expand out the original into nCopies copies. Normally all messages within the copy tree are also copied. If the flag copyExtMsgs is true, then all msgs going out are also copied.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Shell.move">
-<tt class="descname">move</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.move" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) handleMove( Id orig, Id newParent ): moves an Element to a new parent</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Shell.addMsg">
-<tt class="descname">addMsg</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.addMsg" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Makes a msg. Arguments are: msgtype, src object, src field, dest object, dest field</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Shell.quit">
-<tt class="descname">quit</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.quit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Stops simulation running and quits the simulator</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Shell.useClock">
-<tt class="descname">useClock</tt><big>(</big><big>)</big><a class="headerlink" href="#Shell.useClock" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Deals with assignment of path to a given clock. Arguments: path, field, tick number.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="SingleMsg">
-<em class="property">class </em><tt class="descname">SingleMsg</tt><a class="headerlink" href="#SingleMsg" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="SingleMsg.setI1">
-<tt class="descname">setI1</tt><big>(</big><big>)</big><a class="headerlink" href="#SingleMsg.setI1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SingleMsg.getI1">
-<tt class="descname">getI1</tt><big>(</big><big>)</big><a class="headerlink" href="#SingleMsg.getI1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SingleMsg.setI2">
-<tt class="descname">setI2</tt><big>(</big><big>)</big><a class="headerlink" href="#SingleMsg.setI2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SingleMsg.getI2">
-<tt class="descname">getI2</tt><big>(</big><big>)</big><a class="headerlink" href="#SingleMsg.getI2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SingleMsg.i1">
-<tt class="descname">i1</tt><a class="headerlink" href="#SingleMsg.i1" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Index of source object.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SingleMsg.i2">
-<tt class="descname">i2</tt><a class="headerlink" href="#SingleMsg.i2" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Index of dest object.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="SparseMsg">
-<em class="property">class </em><tt class="descname">SparseMsg</tt><a class="headerlink" href="#SparseMsg" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="SparseMsg.getNumRows">
-<tt class="descname">getNumRows</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getNumRows" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.getNumColumns">
-<tt class="descname">getNumColumns</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getNumColumns" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.getNumEntries">
-<tt class="descname">getNumEntries</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getNumEntries" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.setProbability">
-<tt class="descname">setProbability</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.setProbability" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.getProbability">
-<tt class="descname">getProbability</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getProbability" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.setSeed">
-<tt class="descname">setSeed</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.setSeed" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.getSeed">
-<tt class="descname">getSeed</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.getSeed" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.setRandomConnectivity">
-<tt class="descname">setRandomConnectivity</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.setRandomConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns connectivity with specified probability and seed</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.setEntry">
-<tt class="descname">setEntry</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.setEntry" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns single row,column value</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.unsetEntry">
-<tt class="descname">unsetEntry</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.unsetEntry" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Clears single row,column entry</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.clear">
-<tt class="descname">clear</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.clear" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Clears out the entire matrix</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.transpose">
-<tt class="descname">transpose</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.transpose" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Transposes the sparse matrix</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.pairFill">
-<tt class="descname">pairFill</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.pairFill" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Fills entire matrix using pairs of (x,y) indices to indicate presence of a connection. If the target is a FieldElement itautomagically assigns FieldIndices.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SparseMsg.tripletFill">
-<tt class="descname">tripletFill</tt><big>(</big><big>)</big><a class="headerlink" href="#SparseMsg.tripletFill" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Fills entire matrix using triplets of (x,y,fieldIndex) to fully specify every connection in the sparse matrix.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SparseMsg.numRows">
-<tt class="descname">numRows</tt><a class="headerlink" href="#SparseMsg.numRows" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of rows in matrix.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SparseMsg.numColumns">
-<tt class="descname">numColumns</tt><a class="headerlink" href="#SparseMsg.numColumns" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of columns in matrix.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SparseMsg.numEntries">
-<tt class="descname">numEntries</tt><a class="headerlink" href="#SparseMsg.numEntries" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of Entries in matrix.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SparseMsg.probability">
-<tt class="descname">probability</tt><a class="headerlink" href="#SparseMsg.probability" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) connection probability for random connectivity.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SparseMsg.seed">
-<tt class="descname">seed</tt><a class="headerlink" href="#SparseMsg.seed" title="Permalink to this definition">¶</a></dt>
-<dd><p>long (<em>value field</em>) Random number seed for generating probabilistic connectivity.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Species">
-<em class="property">class </em><tt class="descname">Species</tt><a class="headerlink" href="#Species" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="Species.pool">
-<tt class="descname">pool</tt><a class="headerlink" href="#Species.pool" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Connects to pools of this Species type</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Species.setMolWt">
-<tt class="descname">setMolWt</tt><big>(</big><big>)</big><a class="headerlink" href="#Species.setMolWt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Species.getMolWt">
-<tt class="descname">getMolWt</tt><big>(</big><big>)</big><a class="headerlink" href="#Species.getMolWt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Species.handleMolWtRequest">
-<tt class="descname">handleMolWtRequest</tt><big>(</big><big>)</big><a class="headerlink" href="#Species.handleMolWtRequest" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle requests for molWt.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Species.molWtOut">
-<tt class="descname">molWtOut</tt><a class="headerlink" href="#Species.molWtOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) returns molWt.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Species.molWt">
-<tt class="descname">molWt</tt><a class="headerlink" href="#Species.molWt" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Molecular weight of species</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="SpikeGen">
-<em class="property">class </em><tt class="descname">SpikeGen</tt><a class="headerlink" href="#SpikeGen" title="Permalink to this definition">¶</a></dt>
-<dd><p>SpikeGen object, for detecting threshold crossings.The threshold detection can work in multiple modes.</p>
-<blockquote>
-<div>If the refractT < 0.0, then it fires an event only at the rising edge of the input voltage waveform</div></blockquote>
-<dl class="attribute">
-<dt id="SpikeGen.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#SpikeGen.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.Vm">
-<tt class="descname">Vm</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.Vm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.setThreshold">
-<tt class="descname">setThreshold</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.setThreshold" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.getThreshold">
-<tt class="descname">getThreshold</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getThreshold" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.setRefractT">
-<tt class="descname">setRefractT</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.setRefractT" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.getRefractT">
-<tt class="descname">getRefractT</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getRefractT" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.setAbs_refract">
-<tt class="descname">setAbs_refract</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.setAbs_refract" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.getAbs_refract">
-<tt class="descname">getAbs_refract</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getAbs_refract" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.getHasFired">
-<tt class="descname">getHasFired</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getHasFired" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.setEdgeTriggered">
-<tt class="descname">setEdgeTriggered</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.setEdgeTriggered" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpikeGen.getEdgeTriggered">
-<tt class="descname">getEdgeTriggered</tt><big>(</big><big>)</big><a class="headerlink" href="#SpikeGen.getEdgeTriggered" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SpikeGen.spikeOut">
-<tt class="descname">spikeOut</tt><a class="headerlink" href="#SpikeGen.spikeOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out a trigger for an event.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SpikeGen.threshold">
-<tt class="descname">threshold</tt><a class="headerlink" href="#SpikeGen.threshold" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Spiking threshold, must cross it going up</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SpikeGen.refractT">
-<tt class="descname">refractT</tt><a class="headerlink" href="#SpikeGen.refractT" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Refractory Time.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SpikeGen.abs_refract">
-<tt class="descname">abs_refract</tt><a class="headerlink" href="#SpikeGen.abs_refract" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Absolute refractory time. Synonym for refractT.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SpikeGen.hasFired">
-<tt class="descname">hasFired</tt><a class="headerlink" href="#SpikeGen.hasFired" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) True if SpikeGen has just fired</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SpikeGen.edgeTriggered">
-<tt class="descname">edgeTriggered</tt><a class="headerlink" href="#SpikeGen.edgeTriggered" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) When edgeTriggered = 0, the SpikeGen will fire an event in each timestep while incoming Vm is > threshold and at least abs_refracttime has passed since last event. This may be problematic if the incoming Vm remains above threshold for longer than abs_refract. Setting edgeTriggered to 1 resolves this as the SpikeGen generatesan event only on the rising edge of the incoming Vm and will remain idle unless the incoming Vm goes below threshold.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="SpineMesh">
-<em class="property">class </em><tt class="descname">SpineMesh</tt><a class="headerlink" href="#SpineMesh" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="SpineMesh.getParentVoxel">
-<tt class="descname">getParentVoxel</tt><big>(</big><big>)</big><a class="headerlink" href="#SpineMesh.getParentVoxel" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SpineMesh.spineList">
-<tt class="descname">spineList</tt><big>(</big><big>)</big><a class="headerlink" href="#SpineMesh.spineList" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Specifies the list of electrical compartments for the spine,and the associated parent voxelArguments: cell container, shaft compartments, head compartments, parent voxel index</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SpineMesh.parentVoxel">
-<tt class="descname">parentVoxel</tt><a class="headerlink" href="#SpineMesh.parentVoxel" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int> (<em>value field</em>) Vector of indices of proximal voxels within this mesh.Spines are at present modeled with just one compartment,so each entry in this vector is always set to EMPTY == -1U</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Stats">
-<em class="property">class </em><tt class="descname">Stats</tt><a class="headerlink" href="#Stats" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="Stats.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Stats.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stats.getMean">
-<tt class="descname">getMean</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.getMean" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stats.getSdev">
-<tt class="descname">getSdev</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.getSdev" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stats.getSum">
-<tt class="descname">getSum</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.getSum" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stats.getNum">
-<tt class="descname">getNum</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.getNum" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stats.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stats.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Stats.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">process</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">reinit</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stats.mean">
-<tt class="descname">mean</tt><a class="headerlink" href="#Stats.mean" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Mean of all sampled values.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stats.sdev">
-<tt class="descname">sdev</tt><a class="headerlink" href="#Stats.sdev" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Standard Deviation of all sampled values.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stats.sum">
-<tt class="descname">sum</tt><a class="headerlink" href="#Stats.sum" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Sum of all sampled values.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stats.num">
-<tt class="descname">num</tt><a class="headerlink" href="#Stats.num" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of all sampled values.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="SteadyState">
-<em class="property">class </em><tt class="descname">SteadyState</tt><a class="headerlink" href="#SteadyState" title="Permalink to this definition">¶</a></dt>
-<dd><p>SteadyState: works out a steady-state value for a reaction system. It uses GSL heavily, and isn’t even compiled if the flag isn’t set. It finds the ss value closest to the initial conditions, defined by current molecular concentrations.If you want to find multiple stable states, use the MultiStable object,which operates a SteadyState object to find multiple states.If you want to carry out a dose-response calculation, use the DoseResponse object.If you want to follow a stable state in phase space, use the StateTrajectory object.</p>
-<dl class="method">
-<dt id="SteadyState.setStoich">
-<tt class="descname">setStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setStoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getStoich">
-<tt class="descname">getStoich</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getStoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getBadStoichiometry">
-<tt class="descname">getBadStoichiometry</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getBadStoichiometry" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getIsInitialized">
-<tt class="descname">getIsInitialized</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getIsInitialized" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getNIter">
-<tt class="descname">getNIter</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getNIter" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getStatus">
-<tt class="descname">getStatus</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getStatus" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.setMaxIter">
-<tt class="descname">setMaxIter</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setMaxIter" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getMaxIter">
-<tt class="descname">getMaxIter</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getMaxIter" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.setConvergenceCriterion">
-<tt class="descname">setConvergenceCriterion</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setConvergenceCriterion" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getConvergenceCriterion">
-<tt class="descname">getConvergenceCriterion</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getConvergenceCriterion" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getNumVarPools">
-<tt class="descname">getNumVarPools</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getNumVarPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getRank">
-<tt class="descname">getRank</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getRank" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getStateType">
-<tt class="descname">getStateType</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getStateType" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getNNegEigenvalues">
-<tt class="descname">getNNegEigenvalues</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getNNegEigenvalues" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getNPosEigenvalues">
-<tt class="descname">getNPosEigenvalues</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getNPosEigenvalues" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getSolutionStatus">
-<tt class="descname">getSolutionStatus</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getSolutionStatus" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.setTotal">
-<tt class="descname">setTotal</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setTotal" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getTotal">
-<tt class="descname">getTotal</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getTotal" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.getEigenvalues">
-<tt class="descname">getEigenvalues</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.getEigenvalues" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.setupMatrix">
-<tt class="descname">setupMatrix</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.setupMatrix" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) This function initializes and rebuilds the matrices used in the calculation.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.settle">
-<tt class="descname">settle</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.settle" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Finds the nearest steady state to the current initial conditions. This function rebuilds the entire calculation only if the object has not yet been initialized.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.resettle">
-<tt class="descname">resettle</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.resettle" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Finds the nearest steady state to the current initial conditions. This function rebuilds the entire calculation</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.showMatrices">
-<tt class="descname">showMatrices</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.showMatrices" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Utility function to show the matrices derived for the calculations on the reaction system. Shows the Nr, gamma, and total matrices</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SteadyState.randomInit">
-<tt class="descname">randomInit</tt><big>(</big><big>)</big><a class="headerlink" href="#SteadyState.randomInit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Generate random initial conditions consistent with the massconservation rules. Typically invoked in order to scanstates</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.stoich">
-<tt class="descname">stoich</tt><a class="headerlink" href="#SteadyState.stoich" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Specify the Id of the stoichiometry system to use</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.badStoichiometry">
-<tt class="descname">badStoichiometry</tt><a class="headerlink" href="#SteadyState.badStoichiometry" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Bool: True if there is a problem with the stoichiometry</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.isInitialized">
-<tt class="descname">isInitialized</tt><a class="headerlink" href="#SteadyState.isInitialized" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) True if the model has been initialized successfully</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.nIter">
-<tt class="descname">nIter</tt><a class="headerlink" href="#SteadyState.nIter" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of iterations done by steady state solver</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.status">
-<tt class="descname">status</tt><a class="headerlink" href="#SteadyState.status" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Status of solver</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.maxIter">
-<tt class="descname">maxIter</tt><a class="headerlink" href="#SteadyState.maxIter" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Max permissible number of iterations to try before giving up</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.convergenceCriterion">
-<tt class="descname">convergenceCriterion</tt><a class="headerlink" href="#SteadyState.convergenceCriterion" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Fractional accuracy required to accept convergence</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.numVarPools">
-<tt class="descname">numVarPools</tt><a class="headerlink" href="#SteadyState.numVarPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of variable molecules in reaction system.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.rank">
-<tt class="descname">rank</tt><a class="headerlink" href="#SteadyState.rank" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of independent molecules in reaction system</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.stateType">
-<tt class="descname">stateType</tt><a class="headerlink" href="#SteadyState.stateType" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) 0: stable; 1: unstable; 2: saddle; 3: osc?; 4: one near-zero eigenvalue; 5: other</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.nNegEigenvalues">
-<tt class="descname">nNegEigenvalues</tt><a class="headerlink" href="#SteadyState.nNegEigenvalues" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of negative eigenvalues: indicates type of solution</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.nPosEigenvalues">
-<tt class="descname">nPosEigenvalues</tt><a class="headerlink" href="#SteadyState.nPosEigenvalues" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of positive eigenvalues: indicates type of solution</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.solutionStatus">
-<tt class="descname">solutionStatus</tt><a class="headerlink" href="#SteadyState.solutionStatus" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) 0: Good; 1: Failed to find steady states; 2: Failed to find eigenvalues</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.total">
-<tt class="descname">total</tt><a class="headerlink" href="#SteadyState.total" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Totals table for conservation laws. The exact mapping ofthis to various sums of molecules is given by the conservation matrix, and is currently a bit opaque.The value of ‘total’ is set to initial conditions whenthe ‘SteadyState::settle’ function is called.Assigning values to the total is a special operation:it rescales the concentrations of all the affectedmolecules so that they are at the specified total.This happens the next time ‘settle’ is called.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SteadyState.eigenvalues">
-<tt class="descname">eigenvalues</tt><a class="headerlink" href="#SteadyState.eigenvalues" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Eigenvalues computed for steady state</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="StimulusTable">
-<em class="property">class </em><tt class="descname">StimulusTable</tt><a class="headerlink" href="#StimulusTable" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="StimulusTable.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#StimulusTable.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.setStartTime">
-<tt class="descname">setStartTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setStartTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.getStartTime">
-<tt class="descname">getStartTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getStartTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.setStopTime">
-<tt class="descname">setStopTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setStopTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.getStopTime">
-<tt class="descname">getStopTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getStopTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.setLoopTime">
-<tt class="descname">setLoopTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setLoopTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.getLoopTime">
-<tt class="descname">getLoopTime</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getLoopTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.setStepSize">
-<tt class="descname">setStepSize</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setStepSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.getStepSize">
-<tt class="descname">getStepSize</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getStepSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.setStepPosition">
-<tt class="descname">setStepPosition</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setStepPosition" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.getStepPosition">
-<tt class="descname">getStepPosition</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getStepPosition" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.setDoLoop">
-<tt class="descname">setDoLoop</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.setDoLoop" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.getDoLoop">
-<tt class="descname">getDoLoop</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.getDoLoop" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="StimulusTable.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#StimulusTable.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="StimulusTable.output">
-<tt class="descname">output</tt><a class="headerlink" href="#StimulusTable.output" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out tabulated data according to lookup parameters.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="StimulusTable.startTime">
-<tt class="descname">startTime</tt><a class="headerlink" href="#StimulusTable.startTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Start time used when table is emitting values. For lookupvalues below this, the table just sends out its zero entry.Corresponds to zeroth entry of table.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="StimulusTable.stopTime">
-<tt class="descname">stopTime</tt><a class="headerlink" href="#StimulusTable.stopTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Time to stop emitting values.If time exceeds this, then the table sends out its last entry.The stopTime corresponds to the last entry of table.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="StimulusTable.loopTime">
-<tt class="descname">loopTime</tt><a class="headerlink" href="#StimulusTable.loopTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) If looping, this is the time between successive cycle starts.Defaults to the difference between stopTime and startTime, so that the output waveform cycles with precisely the same duration as the table contents.If larger than stopTime - startTime, then it pauses at the last table value till it is time to go around again.If smaller than stopTime - startTime, then it begins the next cycle even before the first one has reached the end of the table.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="StimulusTable.stepSize">
-<tt class="descname">stepSize</tt><a class="headerlink" href="#StimulusTable.stepSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Increment in lookup (x) value on every timestep. If it isless than or equal to zero, the StimulusTable uses the current timeas the lookup value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="StimulusTable.stepPosition">
-<tt class="descname">stepPosition</tt><a class="headerlink" href="#StimulusTable.stepPosition" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Current value of lookup (x) value.If stepSize is less than or equal to zero, this is set tothe current time to use as the lookup value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="StimulusTable.doLoop">
-<tt class="descname">doLoop</tt><a class="headerlink" href="#StimulusTable.doLoop" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Flag: Should it loop around to startTime once it has reachedstopTime. Default (zero) is to do a single pass.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Stoich">
-<em class="property">class </em><tt class="descname">Stoich</tt><a class="headerlink" href="#Stoich" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="Stoich.setPath">
-<tt class="descname">setPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.setPath" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getPath">
-<tt class="descname">getPath</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getPath" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.setKsolve">
-<tt class="descname">setKsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.setKsolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getKsolve">
-<tt class="descname">getKsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getKsolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.setDsolve">
-<tt class="descname">setDsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.setDsolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getDsolve">
-<tt class="descname">getDsolve</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getDsolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.setCompartment">
-<tt class="descname">setCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.setCompartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getCompartment">
-<tt class="descname">getCompartment</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getCompartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getEstimatedDt">
-<tt class="descname">getEstimatedDt</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getEstimatedDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getNumVarPools">
-<tt class="descname">getNumVarPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getNumVarPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getNumAllPools">
-<tt class="descname">getNumAllPools</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getNumAllPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getPoolIdMap">
-<tt class="descname">getPoolIdMap</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getPoolIdMap" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getNumRates">
-<tt class="descname">getNumRates</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getNumRates" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getMatrixEntry">
-<tt class="descname">getMatrixEntry</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getMatrixEntry" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getColumnIndex">
-<tt class="descname">getColumnIndex</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getColumnIndex" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.getRowStart">
-<tt class="descname">getRowStart</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.getRowStart" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Stoich.unzombify">
-<tt class="descname">unzombify</tt><big>(</big><big>)</big><a class="headerlink" href="#Stoich.unzombify" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Restore all zombies to their native state</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.path">
-<tt class="descname">path</tt><a class="headerlink" href="#Stoich.path" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) Wildcard path for reaction system handled by Stoich</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.ksolve">
-<tt class="descname">ksolve</tt><a class="headerlink" href="#Stoich.ksolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Id of Kinetic reaction solver class that works with this Stoich. Must be of class Ksolve, or Gsolve (at present) Must be assigned before the path is set.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.dsolve">
-<tt class="descname">dsolve</tt><a class="headerlink" href="#Stoich.dsolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Id of Diffusion solver class that works with this Stoich. Must be of class Dsolve If left unset then the system will be assumed to work in a non-diffusive, well-stirred cell. If it is going to be used it must be assigned before the path is set.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.compartment">
-<tt class="descname">compartment</tt><a class="headerlink" href="#Stoich.compartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>Id (<em>value field</em>) Id of chemical compartment class that works with this Stoich. Must be derived from class ChemCompt. If left unset then the system will be assumed to work in a non-diffusive, well-stirred cell. If it is going to be used it must be assigned before the path is set.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.estimatedDt">
-<tt class="descname">estimatedDt</tt><a class="headerlink" href="#Stoich.estimatedDt" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Estimated timestep for reac system based on Euler error</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.numVarPools">
-<tt class="descname">numVarPools</tt><a class="headerlink" href="#Stoich.numVarPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of time-varying pools to be computed by the numerical engine</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.numAllPools">
-<tt class="descname">numAllPools</tt><a class="headerlink" href="#Stoich.numAllPools" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Total number of pools handled by the numerical engine. This includes variable ones, buffered ones, and functions</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.poolIdMap">
-<tt class="descname">poolIdMap</tt><a class="headerlink" href="#Stoich.poolIdMap" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int> (<em>value field</em>) Map to look up the index of the pool from its Id.poolIndex = poolIdMap[ Id::value() - poolOffset ] where the poolOffset is the smallest Id::value. poolOffset is passed back as the last entry of this vector. Any Ids that are not pools return EMPTY=~0.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.numRates">
-<tt class="descname">numRates</tt><a class="headerlink" href="#Stoich.numRates" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Total number of rate terms in the reaction system.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.matrixEntry">
-<tt class="descname">matrixEntry</tt><a class="headerlink" href="#Stoich.matrixEntry" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<int> (<em>value field</em>) The non-zero matrix entries in the sparse matrix. Theircolumn indices are in a separate vector and the rowinformatino in a third</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.columnIndex">
-<tt class="descname">columnIndex</tt><a class="headerlink" href="#Stoich.columnIndex" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int> (<em>value field</em>) Column Index of each matrix entry</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Stoich.rowStart">
-<tt class="descname">rowStart</tt><a class="headerlink" href="#Stoich.rowStart" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<unsigned int> (<em>value field</em>) Row start for each block of entries and column indices</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="SumFunc">
-<em class="property">class </em><tt class="descname">SumFunc</tt><a class="headerlink" href="#SumFunc" title="Permalink to this definition">¶</a></dt>
-<dd><p>SumFunc object. Adds up all inputs</p>
-</dd></dl>
-
-<dl class="class">
-<dt id="SymCompartment">
-<em class="property">class </em><tt class="descname">SymCompartment</tt><a class="headerlink" href="#SymCompartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>SymCompartment object, for branching neuron models. In symmetric</p>
-<p>compartments the axial resistance is equally divided on two sides of</p>
-<blockquote>
-<div><p>you must use a fixed-width font like Courier for correct rendition of the diagrams below.]</p>
-<blockquote>
-<div><blockquote>
-<div>Ra/2 B Ra/2</div></blockquote>
-<p>A-///_____///– C</p>
-<blockquote>
-<div><blockquote>
-<div><blockquote>
-<div><blockquote>
-<div><div class="line-block">
-<div class="line"><br /></div>
-</div>
-</div></blockquote>
-<p>____|____</p>
-</div></blockquote>
-<div class="line-block">
-<div class="line"><a href="#id1"><span class="problematic" id="id2">|</span></a></div>
-</div>
-<div class="line-block">
-<div class="line"></div>
-</div>
-<div class="line-block">
-<div class="line">/ Rm</div>
-</div>
-</div></blockquote>
-<p>—- Cm </p>
-<p>—- /</p>
-<blockquote>
-<div><div class="line-block">
-<div class="line"><a href="#id3"><span class="problematic" id="id4">|</span></a></div>
-</div>
-<div class="line-block">
-<div class="line">_____</div>
-</div>
-<div class="line-block">
-<div class="line">— Em</div>
-</div>
-<p><a href="#id11"><span class="problematic" id="id12">|_________|</span></a></p>
-<blockquote>
-<div><blockquote>
-<div><div class="line-block">
-<div class="line"><br /></div>
-</div>
-</div></blockquote>
-<p>__|__</p>
-</div></blockquote>
-</div></blockquote>
-</div></blockquote>
-</div></blockquote>
-</div></blockquote>
-<p>In case of branching, the B-C part of the parent’s axial resistance</p>
-<p>forms a Y with the A-B part of the children.</p>
-<blockquote>
-<div><blockquote>
-<div><blockquote>
-<div><p>B’</p>
-<div class="line-block">
-<div class="line"><br /></div>
-</div>
-<p>/</p>
-<p></p>
-<p>/</p>
-<p></p>
-<p>/</p>
-<p><a href="#id5"><span class="problematic" id="id6">|</span></a>A’</p>
-</div></blockquote>
-<p>B |</p>
-</div></blockquote>
-<p>A—–///—–///——<a href="#id7"><span class="problematic" id="id8">|</span></a>C</p>
-<blockquote>
-<div><div class="line-block">
-<div class="line"><br /></div>
-</div>
-<p><a href="#id9"><span class="problematic" id="id10">|</span></a>A”</p>
-<p>/</p>
-<p></p>
-<p>/</p>
-<p></p>
-<p>/</p>
-<div class="line-block">
-<div class="line"><br /></div>
-</div>
-<p>B”</p>
-</div></blockquote>
-</div></blockquote>
-<p>As per basic circuit analysis techniques, the C node is replaced using</p>
-<p>star-mesh transform. This requires all sibling compartments at a</p>
-<p>branch point to be connected via ‘sibling’ messages by the user (or</p>
-<p>by the cell reader in case of prototypes). For the same reason, the</p>
-<p>child compartment must be connected to the parent by</p>
-<p>distal-proximal message pair. The calculation of the</p>
-<p>coefficient for computing equivalent resistances in the mesh is done</p>
-<p>at reinit.</p>
-<dl class="attribute">
-<dt id="SymCompartment.proximal">
-<tt class="descname">proximal</tt><a class="headerlink" href="#SymCompartment.proximal" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message between symmetric compartments.</p>
-</dd></dl>
-
-</dd></dl>
-
-<p>It goes from the proximal end of the current compartment to
-distal end of the compartment closer to the soma.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="distal">
-<tt class="descname">distal</tt><a class="headerlink" href="#distal" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message between symmetric compartments.</p>
-</dd></dl>
-
-</div></blockquote>
-<dl class="docutils">
-<dt>It goes from the distal end of the current compartment to the</dt>
-<dd>proximal end of one further from the soma.</dd>
-</dl>
-<p>The Ra values collected from children and
-sibling nodes are used for computing the equivalent resistance
-between each pair of nodes using star-mesh transformation.
-Mathematically this is the same as the proximal message, but
-the distinction is important for traversal and clarity.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="sibling">
-<tt class="descname">sibling</tt><a class="headerlink" href="#sibling" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message between symmetric compartments.</p>
-</dd></dl>
-
-</div></blockquote>
-<p>Conceptually, this goes from the proximal end of the current
-compartment to the proximal end of a sibling compartment
-on a branch in a dendrite. However,
-this works out to the same as a ‘distal’ message in terms of
-equivalent circuit. The Ra values collected from siblings
-and parent node are used for
-computing the equivalent resistance between each pair of
-nodes using star-mesh transformation.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="sphere">
-<tt class="descname">sphere</tt><a class="headerlink" href="#sphere" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message between a spherical compartment</p>
-</dd></dl>
-
-</div></blockquote>
-<p>(typically soma) and a number of evenly spaced cylindrical
-compartments, typically primary dendrites.
-The sphere contributes the usual Ra/2 to the resistance
-between itself and children. The child compartments
-do not connect across to each other
-through sibling messages. Instead they just connect to the soma
-through the ‘proximalOnly’ message</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="cylinder">
-<tt class="descname">cylinder</tt><a class="headerlink" href="#cylinder" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message between a cylindrical compartment</p>
-</dd></dl>
-
-</div></blockquote>
-<p>(typically a dendrite) and a number of evenly spaced child
-compartments, typically dendritic spines, protruding from the
-curved surface of the cylinder. We assume that the resistance
-from the cylinder curved surface to its axis is negligible.
-The child compartments do not need to connect across to each
-other through sibling messages. Instead they just connect to the
-parent dendrite through the ‘proximalOnly’ message</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="proximalOnly">
-<tt class="descname">proximalOnly</tt><a class="headerlink" href="#proximalOnly" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message between a dendrite and a parent</p>
-</dd></dl>
-
-</div></blockquote>
-<p>compartment whose offspring are spatially separated from each
-other. For example, evenly spaced dendrites emerging from a soma
-or spines emerging from a common parent dendrite. In these cases
-the sibling dendrites do not need to connect to each other
-through ‘sibling’ messages. Instead they just connect to the
-parent compartment (soma or dendrite) through this message</p>
-<blockquote>
-<div><dl class="method">
-<dt id="raxialSym">
-<tt class="descname">raxialSym</tt><big>(</big><big>)</big><a class="headerlink" href="#raxialSym" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="sumRaxial">
-<tt class="descname">sumRaxial</tt><big>(</big><big>)</big><a class="headerlink" href="#sumRaxial" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Expects Ra from other compartment.</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">raxialSym</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment.</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">sumRaxial</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Expects Ra from other compartment.</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">raxialSym</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment.</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">sumRaxial</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Expects Ra from other compartment.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="raxialSphere">
-<tt class="descname">raxialSphere</tt><big>(</big><big>)</big><a class="headerlink" href="#raxialSphere" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment. This is a special case when</p>
-</dd></dl>
-
-</div></blockquote>
-<p>other compartments are evenly distributed on a spherical compartment.</p>
-<blockquote>
-<div><dl class="method">
-<dt id="raxialCylinder">
-<tt class="descname">raxialCylinder</tt><big>(</big><big>)</big><a class="headerlink" href="#raxialCylinder" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment. This is a special case when</p>
-</dd></dl>
-
-</div></blockquote>
-<p>other compartments are evenly distributed on the curved surface of the cylindrical compartment, so we assume that the cylinder does not add any further resistance.</p>
-<blockquote>
-<div><dl class="method">
-<dt>
-<tt class="descname">raxialSphere</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Expects Ra and Vm from other compartment. This is a special case when</p>
-</dd></dl>
-
-</div></blockquote>
-<p>other compartments are evenly distributed on a spherical compartment.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="proximalOut">
-<tt class="descname">proximalOut</tt><a class="headerlink" href="#proximalOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the proximalend of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOutbut provides a logical orientation of the dendrite.One can traverse proximalOut messages to get to the soma.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="sumRaxialOut">
-<tt class="descname">sumRaxialOut</tt><a class="headerlink" href="#sumRaxialOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out Ra</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="distalOut">
-<tt class="descname">distalOut</tt><a class="headerlink" href="#distalOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the distal endof a compartment. This end should be pointed away from thesoma. Mathematically the same as proximalOut, but givesan orientation to the dendrite and helps traversal.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt>
-<tt class="descname">sumRaxialOut</tt></dt>
-<dd><p>double (<em>source message field</em>) Sends out Ra</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt>
-<tt class="descname">distalOut</tt></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the distal endof a compartment. This end should be pointed away from thesoma. Mathematically the same as proximalOut, but givesan orientation to the dendrite and helps traversal.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt>
-<tt class="descname">sumRaxialOut</tt></dt>
-<dd><p>double (<em>source message field</em>) Sends out Ra</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt>
-<tt class="descname">distalOut</tt></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the distal endof a compartment. This end should be pointed away from thesoma. Mathematically the same as proximalOut, but givesan orientation to the dendrite and helps traversal.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="cylinderOut">
-<tt class="descname">cylinderOut</tt><a class="headerlink" href="#cylinderOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm to compartments (typically spines) on thecurved surface of a cylinder. Ra is set to nearly zero,since we assume that the resistance from axis to surface isnegligible.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt>
-<tt class="descname">proximalOut</tt></dt>
-<dd><p>double,double (<em>source message field</em>) Sends out Ra and Vm on each timestep, on the proximalend of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOutbut provides a logical orientation of the dendrite.One can traverse proximalOut messages to get to the soma.</p>
-</dd></dl>
-
-</div></blockquote>
-<dl class="class">
-<dt id="SynChan">
-<em class="property">class </em><tt class="descname">SynChan</tt><a class="headerlink" href="#SynChan" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="SynChan.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#SynChan.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.setTau1">
-<tt class="descname">setTau1</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.setTau1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.getTau1">
-<tt class="descname">getTau1</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.getTau1" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.setTau2">
-<tt class="descname">setTau2</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.setTau2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.getTau2">
-<tt class="descname">getTau2</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.getTau2" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.setNormalizeWeights">
-<tt class="descname">setNormalizeWeights</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.setNormalizeWeights" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.getNormalizeWeights">
-<tt class="descname">getNormalizeWeights</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.getNormalizeWeights" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.activation">
-<tt class="descname">activation</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.activation" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Sometimes we want to continuously activate the channel</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChan.modulator">
-<tt class="descname">modulator</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChan.modulator" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Modulate channel response</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChan.tau1">
-<tt class="descname">tau1</tt><a class="headerlink" href="#SynChan.tau1" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Decay time constant for the synaptic conductance, tau1 >= tau2.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChan.tau2">
-<tt class="descname">tau2</tt><a class="headerlink" href="#SynChan.tau2" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Rise time constant for the synaptic conductance, tau1 >= tau2.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChan.normalizeWeights">
-<tt class="descname">normalizeWeights</tt><a class="headerlink" href="#SynChan.normalizeWeights" title="Permalink to this definition">¶</a></dt>
-<dd><p>bool (<em>value field</em>) Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="SynChanBase">
-<em class="property">class </em><tt class="descname">SynChanBase</tt><a class="headerlink" href="#SynChanBase" title="Permalink to this definition">¶</a></dt>
-<dd><p>SynChanBase: Base class for assorted ion channels.Presents a common interface for all of them.</p>
-<dl class="attribute">
-<dt id="SynChanBase.channel">
-<tt class="descname">channel</tt><a class="headerlink" href="#SynChanBase.channel" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChanBase.ghk">
-<tt class="descname">ghk</tt><a class="headerlink" href="#SynChanBase.ghk" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Message to Goldman-Hodgkin-Katz object</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.Vm">
-<tt class="descname">Vm</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.Vm" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<tt class="descname">Vm</tt><big>(</big><big>)</big></dt>
-<dd><p>(<em>destination message field</em>) Handles Vm message coming in from compartment</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.setGbar">
-<tt class="descname">setGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.setGbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.getGbar">
-<tt class="descname">getGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getGbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.setEk">
-<tt class="descname">setEk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.setEk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.getEk">
-<tt class="descname">getEk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getEk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.setGk">
-<tt class="descname">setGk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.setGk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.getGk">
-<tt class="descname">getGk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getGk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.getIk">
-<tt class="descname">getIk</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getIk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.setBufferTime">
-<tt class="descname">setBufferTime</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.setBufferTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynChanBase.getBufferTime">
-<tt class="descname">getBufferTime</tt><big>(</big><big>)</big><a class="headerlink" href="#SynChanBase.getBufferTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChanBase.channelOut">
-<tt class="descname">channelOut</tt><a class="headerlink" href="#SynChanBase.channelOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>source message field</em>) Sends channel variables Gk and Ek to compartment</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChanBase.permeabilityOut">
-<tt class="descname">permeabilityOut</tt><a class="headerlink" href="#SynChanBase.permeabilityOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Conductance term going out to GHK object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChanBase.IkOut">
-<tt class="descname">IkOut</tt><a class="headerlink" href="#SynChanBase.IkOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Channel current. This message typically goes to concenobjects that keep track of ion concentration.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChanBase.Gbar">
-<tt class="descname">Gbar</tt><a class="headerlink" href="#SynChanBase.Gbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximal channel conductance</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChanBase.Ek">
-<tt class="descname">Ek</tt><a class="headerlink" href="#SynChanBase.Ek" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Reversal potential of channel</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChanBase.Gk">
-<tt class="descname">Gk</tt><a class="headerlink" href="#SynChanBase.Gk" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Channel conductance variable</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChanBase.Ik">
-<tt class="descname">Ik</tt><a class="headerlink" href="#SynChanBase.Ik" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Channel current variable</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynChanBase.bufferTime">
-<tt class="descname">bufferTime</tt><a class="headerlink" href="#SynChanBase.bufferTime" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Duration of spike buffer.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="SynHandler">
-<em class="property">class </em><tt class="descname">SynHandler</tt><a class="headerlink" href="#SynHandler" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="SynHandler.setNumSynapses">
-<tt class="descname">setNumSynapses</tt><big>(</big><big>)</big><a class="headerlink" href="#SynHandler.setNumSynapses" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynHandler.getNumSynapses">
-<tt class="descname">getNumSynapses</tt><big>(</big><big>)</big><a class="headerlink" href="#SynHandler.getNumSynapses" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynHandler.setNumSynapse">
-<tt class="descname">setNumSynapse</tt><big>(</big><big>)</big><a class="headerlink" href="#SynHandler.setNumSynapse" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="SynHandler.getNumSynapse">
-<tt class="descname">getNumSynapse</tt><big>(</big><big>)</big><a class="headerlink" href="#SynHandler.getNumSynapse" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="SynHandler.numSynapses">
-<tt class="descname">numSynapses</tt><a class="headerlink" href="#SynHandler.numSynapses" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of synapses on SynHandler. Duplicate field for num_synapse</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Synapse">
-<em class="property">class </em><tt class="descname">Synapse</tt><a class="headerlink" href="#Synapse" title="Permalink to this definition">¶</a></dt>
-<dd><p>Synapse using ring buffer for events.</p>
-<dl class="method">
-<dt id="Synapse.setWeight">
-<tt class="descname">setWeight</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.setWeight" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Synapse.getWeight">
-<tt class="descname">getWeight</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.getWeight" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Synapse.setDelay">
-<tt class="descname">setDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.setDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Synapse.getDelay">
-<tt class="descname">getDelay</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.getDelay" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Synapse.addSpike">
-<tt class="descname">addSpike</tt><big>(</big><big>)</big><a class="headerlink" href="#Synapse.addSpike" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles arriving spike messages, inserts into event queue.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Synapse.weight">
-<tt class="descname">weight</tt><a class="headerlink" href="#Synapse.weight" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Synaptic weight</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Synapse.delay">
-<tt class="descname">delay</tt><a class="headerlink" href="#Synapse.delay" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Axonal propagation delay to this synapse</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="Table">
-<em class="property">class </em><tt class="descname">Table</tt><a class="headerlink" href="#Table" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="Table.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#Table.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Table.setThreshold">
-<tt class="descname">setThreshold</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.setThreshold" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Table.getThreshold">
-<tt class="descname">getThreshold</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.getThreshold" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Table.input">
-<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.input" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Fills data into table. Also handles data sent back following request</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Table.spike">
-<tt class="descname">spike</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.spike" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Fills spike timings into the Table. Signal has to exceed thresh</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Table.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call, updates internal time stamp.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Table.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#Table.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Table.requestOut">
-<tt class="descname">requestOut</tt><a class="headerlink" href="#Table.requestOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>Pd (<em>source message field</em>) Sends request for a field to target object</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Table.threshold">
-<tt class="descname">threshold</tt><a class="headerlink" href="#Table.threshold" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) threshold used when Table acts as a buffer for spikes</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="TableBase">
-<em class="property">class </em><tt class="descname">TableBase</tt><a class="headerlink" href="#TableBase" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="TableBase.setVector">
-<tt class="descname">setVector</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.setVector" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.getVector">
-<tt class="descname">getVector</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.getVector" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.getOutputValue">
-<tt class="descname">getOutputValue</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.getOutputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.getSize">
-<tt class="descname">getSize</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.getSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.getY">
-<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.getY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.linearTransform">
-<tt class="descname">linearTransform</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.linearTransform" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Linearly scales and offsets data. Scale first, then offset.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.xplot">
-<tt class="descname">xplot</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.xplot" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.plainPlot">
-<tt class="descname">plainPlot</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.plainPlot" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.loadCSV">
-<tt class="descname">loadCSV</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.loadCSV" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.loadXplot">
-<tt class="descname">loadXplot</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.loadXplot" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.loadXplotRange">
-<tt class="descname">loadXplotRange</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.loadXplotRange" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.compareXplot">
-<tt class="descname">compareXplot</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.compareXplot" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Reads a plot from an xplot file and compares with contents of TableBase.Result is put in ‘output’ field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.compareVec">
-<tt class="descname">compareVec</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.compareVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Compares contents of TableBase with a vector of doubles.Result is put in ‘output’ field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TableBase.clearVec">
-<tt class="descname">clearVec</tt><big>(</big><big>)</big><a class="headerlink" href="#TableBase.clearVec" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles request to clear the data vector</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="TableBase.vector">
-<tt class="descname">vector</tt><a class="headerlink" href="#TableBase.vector" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) vector with all table entries</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="TableBase.outputValue">
-<tt class="descname">outputValue</tt><a class="headerlink" href="#TableBase.outputValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Output value holding current table entry or output of a calculation</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="TableBase.size">
-<tt class="descname">size</tt><a class="headerlink" href="#TableBase.size" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="TableBase.y">
-<tt class="descname">y</tt><a class="headerlink" href="#TableBase.y" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Value of table at specified index</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="TimeTable">
-<em class="property">class </em><tt class="descname">TimeTable</tt><a class="headerlink" href="#TimeTable" title="Permalink to this definition">¶</a></dt>
-<dd><p>TimeTable: Read in spike times from file and send out eventOut messages</p>
-<p>at the specified times.</p>
-<dl class="attribute">
-<dt id="TimeTable.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#TimeTable.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message for process and reinit</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TimeTable.setFilename">
-<tt class="descname">setFilename</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.setFilename" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TimeTable.getFilename">
-<tt class="descname">getFilename</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.getFilename" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TimeTable.setMethod">
-<tt class="descname">setMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.setMethod" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TimeTable.getMethod">
-<tt class="descname">getMethod</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.getMethod" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TimeTable.getState">
-<tt class="descname">getState</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.getState" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TimeTable.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handle process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="TimeTable.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#TimeTable.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="TimeTable.eventOut">
-<tt class="descname">eventOut</tt><a class="headerlink" href="#TimeTable.eventOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out spike time if it falls in current timestep.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="TimeTable.filename">
-<tt class="descname">filename</tt><a class="headerlink" href="#TimeTable.filename" title="Permalink to this definition">¶</a></dt>
-<dd><p>string (<em>value field</em>) File to read lookup data from. The file should be contain two columns</p>
-</dd></dl>
-
-</dd></dl>
-
-<p>separated by any space character.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="method">
-<tt class="descname">method</tt><a class="headerlink" href="#method" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) Method to use for filling up the entries. Currently only method 4</p>
-</dd></dl>
-
-</div></blockquote>
-<p>(loading from file) is supported.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="state">
-<tt class="descname">state</tt><a class="headerlink" href="#state" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Current state of the time table.</p>
-</dd></dl>
-
-</div></blockquote>
-<dl class="class">
-<dt id="Unsigned">
-<em class="property">class </em><tt class="descname">Unsigned</tt><a class="headerlink" href="#Unsigned" title="Permalink to this definition">¶</a></dt>
-<dd><p>Variable for storing values.</p>
-<dl class="method">
-<dt id="Unsigned.setValue">
-<tt class="descname">setValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Unsigned.setValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="Unsigned.getValue">
-<tt class="descname">getValue</tt><big>(</big><big>)</big><a class="headerlink" href="#Unsigned.getValue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="Unsigned.value">
-<tt class="descname">value</tt><a class="headerlink" href="#Unsigned.value" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned long (<em>value field</em>) Variable value</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="VClamp">
-<em class="property">class </em><tt class="descname">VClamp</tt><a class="headerlink" href="#VClamp" title="Permalink to this definition">¶</a></dt>
-<dd><blockquote>
-<div><p>Voltage clamp object for holding neuronal compartments at a specific voltage. This implementation uses a builtin RC circuit to filter the</p>
-<p>command input and then use a PID to bring the sensed voltage (Vm from</p>
-<p>compartment) to the filtered command potential.</p>
-<blockquote>
-<div>Connect the <cite>currentOut</cite> source of VClamp to <cite>injectMsg</cite></div></blockquote>
-<p>dest of Compartment. Connect the <cite>VmOut</cite> source of Compartment to</p>
-<p><cite>set_sensed</cite> dest of VClamp. Either set <cite>command</cite> field to a</p>
-<p>fixed value, or connect an appropriate source of command potential</p>
-<p>(like the <cite>outputOut</cite> message of an appropriately configured</p>
-<p>PulseGen) to <cite>set_command</cite> dest.</p>
-<blockquote>
-<div>The default settings for the RC filter and PID controller should be</div></blockquote>
-<p>time constant of RC filter, tau = 5 * dt</p>
-<p>proportional gain of PID, gain = Cm/dt where Cm is the membrane</p>
-<blockquote>
-<div>capacitance of the compartment</div></blockquote>
-<p>integration time of PID, ti = dt</p>
-<p>derivative time of PID, td = 0</p>
-<dl class="attribute">
-<dt id="VClamp.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#VClamp.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message to receive Process messages from the scheduler</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.getCommand">
-<tt class="descname">getCommand</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getCommand" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.getCurrent">
-<tt class="descname">getCurrent</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getCurrent" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.getSensed">
-<tt class="descname">getSensed</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getSensed" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.setMode">
-<tt class="descname">setMode</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.getMode">
-<tt class="descname">getMode</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.setTi">
-<tt class="descname">setTi</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setTi" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.getTi">
-<tt class="descname">getTi</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getTi" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.setTd">
-<tt class="descname">setTd</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setTd" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.getTd">
-<tt class="descname">getTd</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getTd" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.setTau">
-<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.getTau">
-<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.setGain">
-<tt class="descname">setGain</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.setGain" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.getGain">
-<tt class="descname">getGain</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.getGain" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.sensedIn">
-<tt class="descname">sensedIn</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.sensedIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) The <cite>VmOut</cite> message of the Compartment object should be connected</p>
-</dd></dl>
-
-</div></blockquote>
-<p>here.</p>
-<blockquote>
-<div><dl class="method">
-<dt id="VClamp.commandIn">
-<tt class="descname">commandIn</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.commandIn" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) The command voltage source should be connected to this.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘process’ call on each time step.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VClamp.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#VClamp.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles ‘reinit’ call</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VClamp.currentOut">
-<tt class="descname">currentOut</tt><a class="headerlink" href="#VClamp.currentOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Sends out current output of the clamping circuit. This should be connected to the <cite>injectMsg</cite> field of a compartment to voltage clamp it.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VClamp.command">
-<tt class="descname">command</tt><a class="headerlink" href="#VClamp.command" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Command input received by the clamp circuit.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VClamp.current">
-<tt class="descname">current</tt><a class="headerlink" href="#VClamp.current" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) The amount of current injected by the clamp into the membrane.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VClamp.sensed">
-<tt class="descname">sensed</tt><a class="headerlink" href="#VClamp.sensed" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Membrane potential read from compartment.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VClamp.mode">
-<tt class="descname">mode</tt><a class="headerlink" href="#VClamp.mode" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Working mode of the PID controller.</p>
-</dd></dl>
-
-</div></blockquote>
-</dd></dl>
-
-<dl class="docutils">
-<dt>mode = 0, standard PID with proportional, integral and derivative</dt>
-<dd>all acting on the error.</dd>
-</dl>
-<p>mode = 1, derivative action based on command input
-mode = 2, proportional action and derivative action are based on
-command input.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="ti">
-<tt class="descname">ti</tt><a class="headerlink" href="#ti" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Integration time of the PID controller. Defaults to 1e9, i.e. integral</p>
-</dd></dl>
-
-</div></blockquote>
-<p>action is negligibly small.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="td">
-<tt class="descname">td</tt><a class="headerlink" href="#td" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Derivative time of the PID controller. This defaults to 0,</p>
-</dd></dl>
-
-</div></blockquote>
-<p>i.e. derivative action is unused.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="tau">
-<tt class="descname">tau</tt><a class="headerlink" href="#tau" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Time constant of the lowpass filter at input of the PID</p>
-</dd></dl>
-
-</div></blockquote>
-<p>controller. This smooths out abrupt changes in the input. Set it to
-5 * dt or more to avoid overshoots.</p>
-<blockquote>
-<div><dl class="attribute">
-<dt id="gain">
-<tt class="descname">gain</tt><a class="headerlink" href="#gain" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Proportional gain of the PID controller.</p>
-</dd></dl>
-
-</div></blockquote>
-<dl class="class">
-<dt id="VectorTable">
-<em class="property">class </em><tt class="descname">VectorTable</tt><a class="headerlink" href="#VectorTable" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="VectorTable.setXdivs">
-<tt class="descname">setXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.setXdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.getXdivs">
-<tt class="descname">getXdivs</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getXdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.setXmin">
-<tt class="descname">setXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.setXmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.getXmin">
-<tt class="descname">getXmin</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getXmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.setXmax">
-<tt class="descname">setXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.setXmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.getXmax">
-<tt class="descname">getXmax</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getXmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.getInvdx">
-<tt class="descname">getInvdx</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getInvdx" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.setTable">
-<tt class="descname">setTable</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.setTable" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.getTable">
-<tt class="descname">getTable</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getTable" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.getLookupvalue">
-<tt class="descname">getLookupvalue</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getLookupvalue" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="VectorTable.getLookupindex">
-<tt class="descname">getLookupindex</tt><big>(</big><big>)</big><a class="headerlink" href="#VectorTable.getLookupindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VectorTable.xdivs">
-<tt class="descname">xdivs</tt><a class="headerlink" href="#VectorTable.xdivs" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int (<em>value field</em>) Number of divisions.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VectorTable.xmin">
-<tt class="descname">xmin</tt><a class="headerlink" href="#VectorTable.xmin" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Minimum value in table.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VectorTable.xmax">
-<tt class="descname">xmax</tt><a class="headerlink" href="#VectorTable.xmax" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximum value in table.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VectorTable.invdx">
-<tt class="descname">invdx</tt><a class="headerlink" href="#VectorTable.invdx" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximum value in table.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VectorTable.table">
-<tt class="descname">table</tt><a class="headerlink" href="#VectorTable.table" title="Permalink to this definition">¶</a></dt>
-<dd><p>vector<double> (<em>value field</em>) The lookup table.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VectorTable.lookupvalue">
-<tt class="descname">lookupvalue</tt><a class="headerlink" href="#VectorTable.lookupvalue" title="Permalink to this definition">¶</a></dt>
-<dd><p>double,double (<em>lookup field</em>) Lookup function that performs interpolation to return a value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="VectorTable.lookupindex">
-<tt class="descname">lookupindex</tt><a class="headerlink" href="#VectorTable.lookupindex" title="Permalink to this definition">¶</a></dt>
-<dd><p>unsigned int,double (<em>lookup field</em>) Lookup function that returns value by index.</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="ZombieBufPool">
-<em class="property">class </em><tt class="descname">ZombieBufPool</tt><a class="headerlink" href="#ZombieBufPool" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="ZombieCaConc">
-<em class="property">class </em><tt class="descname">ZombieCaConc</tt><a class="headerlink" href="#ZombieCaConc" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="attribute">
-<dt id="ZombieCaConc.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#ZombieCaConc.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) Shared message to receive Process message from scheduler</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.setCa">
-<tt class="descname">setCa</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setCa" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.getCa">
-<tt class="descname">getCa</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getCa" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.setCaBasal">
-<tt class="descname">setCaBasal</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setCaBasal" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.getCaBasal">
-<tt class="descname">getCaBasal</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getCaBasal" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.setCa_base">
-<tt class="descname">setCa_base</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setCa_base" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.getCa_base">
-<tt class="descname">getCa_base</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getCa_base" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.setTau">
-<tt class="descname">setTau</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.getTau">
-<tt class="descname">getTau</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getTau" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.setB">
-<tt class="descname">setB</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.getB">
-<tt class="descname">getB</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getB" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.setThick">
-<tt class="descname">setThick</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setThick" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.getThick">
-<tt class="descname">getThick</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getThick" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.setCeiling">
-<tt class="descname">setCeiling</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setCeiling" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.getCeiling">
-<tt class="descname">getCeiling</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getCeiling" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.setFloor">
-<tt class="descname">setFloor</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.setFloor" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.getFloor">
-<tt class="descname">getFloor</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.getFloor" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.current">
-<tt class="descname">current</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.current" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Calcium Ion current, due to be converted to conc.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.currentFraction">
-<tt class="descname">currentFraction</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.currentFraction" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Fraction of total Ion current, that is carried by Ca2+.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.increase">
-<tt class="descname">increase</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.increase" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Any input current that increases the concentration.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.decrease">
-<tt class="descname">decrease</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.decrease" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Any input current that decreases the concentration.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieCaConc.basal">
-<tt class="descname">basal</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieCaConc.basal" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Synonym for assignment of basal conc.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieCaConc.concOut">
-<tt class="descname">concOut</tt><a class="headerlink" href="#ZombieCaConc.concOut" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>source message field</em>) Concentration of Ca in pool</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieCaConc.Ca">
-<tt class="descname">Ca</tt><a class="headerlink" href="#ZombieCaConc.Ca" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Calcium concentration.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieCaConc.CaBasal">
-<tt class="descname">CaBasal</tt><a class="headerlink" href="#ZombieCaConc.CaBasal" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Basal Calcium concentration.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieCaConc.Ca_base">
-<tt class="descname">Ca_base</tt><a class="headerlink" href="#ZombieCaConc.Ca_base" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Basal Calcium concentration, synonym for CaBasal</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieCaConc.tau">
-<tt class="descname">tau</tt><a class="headerlink" href="#ZombieCaConc.tau" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Settling time for Ca concentration</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieCaConc.B">
-<tt class="descname">B</tt><a class="headerlink" href="#ZombieCaConc.B" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Volume scaling factor</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieCaConc.thick">
-<tt class="descname">thick</tt><a class="headerlink" href="#ZombieCaConc.thick" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Thickness of Ca shell.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieCaConc.ceiling">
-<tt class="descname">ceiling</tt><a class="headerlink" href="#ZombieCaConc.ceiling" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieCaConc.floor">
-<tt class="descname">floor</tt><a class="headerlink" href="#ZombieCaConc.floor" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Floor value for Ca concentration. If Ca < floor, Ca = floor</p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="ZombieCompartment">
-<em class="property">class </em><tt class="descname">ZombieCompartment</tt><a class="headerlink" href="#ZombieCompartment" title="Permalink to this definition">¶</a></dt>
-<dd><p>Compartment object, for branching neuron models.</p>
-</dd></dl>
-
-<dl class="class">
-<dt id="ZombieEnz">
-<em class="property">class </em><tt class="descname">ZombieEnz</tt><a class="headerlink" href="#ZombieEnz" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="ZombieFuncPool">
-<em class="property">class </em><tt class="descname">ZombieFuncPool</tt><a class="headerlink" href="#ZombieFuncPool" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="ZombieFuncPool.input">
-<tt class="descname">input</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieFuncPool.input" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles input to control value of <a href="#id25"><span class="problematic" id="id26">n_</span></a></p>
-</dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="ZombieHHChannel">
-<em class="property">class </em><tt class="descname">ZombieHHChannel</tt><a class="headerlink" href="#ZombieHHChannel" title="Permalink to this definition">¶</a></dt>
-<dd><blockquote>
-<div><dl class="attribute">
-<dt id="ZombieHHChannel.proc">
-<tt class="descname">proc</tt><a class="headerlink" href="#ZombieHHChannel.proc" title="Permalink to this definition">¶</a></dt>
-<dd><p>void (<em>shared message field</em>) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.</p>
-</dd></dl>
-
-</div></blockquote>
-<p>The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.</p>
-<blockquote>
-<div><dl class="method">
-<dt id="ZombieHHChannel.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles process call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.reinit">
-<tt class="descname">reinit</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.reinit" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Handles reinit call</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setGbar">
-<tt class="descname">setGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setGbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getGbar">
-<tt class="descname">getGbar</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getGbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setEk">
-<tt class="descname">setEk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setEk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getEk">
-<tt class="descname">getEk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getEk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setGk">
-<tt class="descname">setGk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setGk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getGk">
-<tt class="descname">getGk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getGk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getIk">
-<tt class="descname">getIk</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getIk" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setXpower">
-<tt class="descname">setXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setXpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getXpower">
-<tt class="descname">getXpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getXpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setYpower">
-<tt class="descname">setYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setYpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getYpower">
-<tt class="descname">getYpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getYpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setZpower">
-<tt class="descname">setZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setZpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getZpower">
-<tt class="descname">getZpower</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getZpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setInstant">
-<tt class="descname">setInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setInstant" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getInstant">
-<tt class="descname">getInstant</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getInstant" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setX">
-<tt class="descname">setX</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getX">
-<tt class="descname">getX</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setY">
-<tt class="descname">setY</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getY">
-<tt class="descname">getY</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setZ">
-<tt class="descname">setZ</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getZ">
-<tt class="descname">getZ</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setUseConcentration">
-<tt class="descname">setUseConcentration</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setUseConcentration" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns field value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getUseConcentration">
-<tt class="descname">getUseConcentration</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getUseConcentration" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests field value. The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.concen">
-<tt class="descname">concen</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.concen" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Incoming message from Concen object to specific conc to usein the Z gate calculations</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.createGate">
-<tt class="descname">createGate</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.createGate" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Function to create specified gate.Argument: Gate type [X Y Z]</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setNumGateX">
-<tt class="descname">setNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setNumGateX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getNumGateX">
-<tt class="descname">getNumGateX</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getNumGateX" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setNumGateY">
-<tt class="descname">setNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setNumGateY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getNumGateY">
-<tt class="descname">getNumGateY</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getNumGateY" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.setNumGateZ">
-<tt class="descname">setNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.setNumGateZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Assigns number of field entries in field array.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="ZombieHHChannel.getNumGateZ">
-<tt class="descname">getNumGateZ</tt><big>(</big><big>)</big><a class="headerlink" href="#ZombieHHChannel.getNumGateZ" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.Gbar">
-<tt class="descname">Gbar</tt><a class="headerlink" href="#ZombieHHChannel.Gbar" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Maximal channel conductance</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.Ek">
-<tt class="descname">Ek</tt><a class="headerlink" href="#ZombieHHChannel.Ek" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Reversal potential of channel</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.Gk">
-<tt class="descname">Gk</tt><a class="headerlink" href="#ZombieHHChannel.Gk" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Channel conductance variable</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.Ik">
-<tt class="descname">Ik</tt><a class="headerlink" href="#ZombieHHChannel.Ik" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Channel current variable</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.Xpower">
-<tt class="descname">Xpower</tt><a class="headerlink" href="#ZombieHHChannel.Xpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Power for X gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.Ypower">
-<tt class="descname">Ypower</tt><a class="headerlink" href="#ZombieHHChannel.Ypower" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Power for Y gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.Zpower">
-<tt class="descname">Zpower</tt><a class="headerlink" href="#ZombieHHChannel.Zpower" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) Power for Z gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.instant">
-<tt class="descname">instant</tt><a class="headerlink" href="#ZombieHHChannel.instant" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.X">
-<tt class="descname">X</tt><a class="headerlink" href="#ZombieHHChannel.X" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) State variable for X gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.Y">
-<tt class="descname">Y</tt><a class="headerlink" href="#ZombieHHChannel.Y" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) State variable for Y gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.Z">
-<tt class="descname">Z</tt><a class="headerlink" href="#ZombieHHChannel.Z" title="Permalink to this definition">¶</a></dt>
-<dd><p>double (<em>value field</em>) State variable for Y gate</p>
-</dd></dl>
-
-<dl class="attribute">
-<dt id="ZombieHHChannel.useConcentration">
-<tt class="descname">useConcentration</tt><a class="headerlink" href="#ZombieHHChannel.useConcentration" title="Permalink to this definition">¶</a></dt>
-<dd><p>int (<em>value field</em>) Flag: when true, use concentration message rather than Vm tocontrol Z gate</p>
-</dd></dl>
-
-</div></blockquote>
-</dd></dl>
-
-<dl class="class">
-<dt id="ZombieMMenz">
-<em class="property">class </em><tt class="descname">ZombieMMenz</tt><a class="headerlink" href="#ZombieMMenz" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="ZombiePool">
-<em class="property">class </em><tt class="descname">ZombiePool</tt><a class="headerlink" href="#ZombiePool" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="ZombieReac">
-<em class="property">class </em><tt class="descname">ZombieReac</tt><a class="headerlink" href="#ZombieReac" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="class">
-<dt id="testSched">
-<em class="property">class </em><tt class="descname">testSched</tt><a class="headerlink" href="#testSched" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="testSched.process">
-<tt class="descname">process</tt><big>(</big><big>)</big><a class="headerlink" href="#testSched.process" title="Permalink to this definition">¶</a></dt>
-<dd><p>(<em>destination message field</em>) handles process call</p>
-</dd></dl>
-
-</dd></dl>
-
-</div>
-
-
- </div>
- </div>
- </div>
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- <title>Getting started with python scripting for MOOSE</title>
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-<div id="header">
-<h1 class="title">Getting started with python scripting for MOOSE</h1>
-<h2 class="author">Subhasis Ray</h2>
-<h3 class="date">December 12, 2012</h3>
-</div>
-<div id="TOC">
-<ul>
-<li><a href="#introduction">Introduction</a></li>
-<li><a href="#importing-moose-and-accessing-built-in-documentation">Importing MOOSE and accessing built-in documentation</a></li>
-<li><a href="#creating-objects-and-traversing-the-object-hierarchy">Creating objects and traversing the object hierarchy</a></li>
-<li><a href="#setting-the-properties-of-elements-accessing-fields">Setting the properties of elements: accessing fields</a></li>
-<li><a href="#putting-them-together-setting-up-connections">Putting them together: setting up connections</a></li>
-<li><a href="#scheduling-and-running-the-simulation">Scheduling and running the simulation</a></li>
-<li><a href="#some-more-details">Some more details</a><ul>
-<li><a href="#ematrix-melement-and-element"><code>ematrix</code>, <code>melement</code> and <code>element</code></a></li>
-<li><a href="#finfos"><code>Finfos</code></a></li>
-</ul></li>
-<li><a href="#moving-on">Moving on</a></li>
-</ul>
-</div>
-<h1 id="introduction"><a href="#introduction">Introduction</a></h1>
-<p>This document describes how to use the <code>moose</code> module in Python scripts or in an interactive Python shell. It aims to give you enough overview to help you start scripting using MOOSE and extract farther information that may be required for advanced work. Knowledge of Python or programming in general will be helpful. If you just want to simulate existing models in one of the supported formats, you can fire the MOOSE GUI and locate the model file using the <code>File</code> menu and load it. The GUI is described <a href="./MooseGuiDocs.html">here</a>. The example code in the boxes can be entered in a Python shell.</p>
-<h1 id="importing-moose-and-accessing-built-in-documentation"><a href="#importing-moose-and-accessing-built-in-documentation">Importing MOOSE and accessing built-in documentation</a></h1>
-<p>In a python script you import modules to access the functionalities they provide.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="ch">import</span> moose</code></pre>
-<p>This makes the <code>moose</code> module available for use in Python. You can use Python's built-in <code>help</code> function to read the top-level documentation for the moose module:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">help</span>(moose)</code></pre>
-<p>This will give you an overview of the module. Press <code>q</code> to exit the pager and get back to the interpreter. You can also access the documentation for individual classes and functions this way.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">help</span>(moose.<span class="ot">connect</span>)</code></pre>
-<p>To list the available functions and classes you can use <code>dir</code> function<a href="#fn1" class="footnoteRef" id="fnref1"><sup>1</sup></a>.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">dir</span>(moose)</code></pre>
-<p>MOOSE has built-in documentation in the C++-source-code independent of Python. The <code>moose</code> module has a separate <code>doc</code> function to extract this documentation.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.doc(moose.Compartment)</code></pre>
-<p>The class level documentation will show whatever the author/maintainer of the class wrote for documentation followed by a list of various kinds of fields and their data types. This can be very useful in an interactive session.</p>
-<p>Each field can have its own detailed documentation, too.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.doc(<span class="st">'Compartment.Rm'</span>)</code></pre>
-<p>Note that you need to put the class-name followed by dot followed by field-name within quotes. Otherwise, <code>moose.doc</code> will receive the field value as parameter and get confused.</p>
-<h1 id="creating-objects-and-traversing-the-object-hierarchy"><a href="#creating-objects-and-traversing-the-object-hierarchy">Creating objects and traversing the object hierarchy</a></h1>
-<p>Different types of biological entities like neurons, enzymes, etc are represented by classes and individual instances of those types are objects of those classes. Objects are the building-blocks of models in MOOSE. We call MOOSE objects <code>element</code> and use object and element interchangeably in the context of MOOSE. Elements are conceptually laid out in a tree-like hierarchical structure. If you are familiar with file system hierarchies in common operating systems, this should be simple.</p>
-<p>At the top of the object hierarchy sits the <code>Shell</code>, equivalent to the root directory in UNIX-based systems and represented by the path <code>/</code>. You can list the existing objects under <code>/</code> using the <code>le</code> function.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.le()</code></pre>
-<p>This shows something like:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> Elements under /
- /Msgs
- /clock
- /classes</code></pre>
-<p><code>Msgs</code>, <code>clock</code> and <code>classes</code> are predefined objects in MOOSE. And each object can contain other objects inside them. You can see them by passing the path of the parent object to <code>le</code>.</p>
-<p>Entering:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.le(<span class="st">'/clock'</span>)</code></pre>
-<p>prints:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> Elements under /clock
- /clock/tick[<span class="dv">0</span>]</code></pre>
-<p>Now let us create some objects of our own. This can be done by invoking MOOSE class constructors (just like regular Python classes).</p>
-<pre class="sourceCode python"><code class="sourceCode python"> model = moose.Neutral(<span class="st">'/model'</span>)</code></pre>
-<p>The above creates a <code>Neutral</code> object named <code>model</code>. <code>Neutral</code> is the most basic class in MOOSE. A <code>Neutral</code> element can act as a container for other elements. We can create something under <code>model</code>:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> soma = moose.Compartment(<span class="st">'/model/soma'</span>)</code></pre>
-<p>Every element has a unique path. This is a concatenation of the names of all the objects one has to traverse starting with the root to reach that element.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.path</code></pre>
-<p>shows you its path:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> /model/soma</code></pre>
-<p>The name of the element can be printed, too.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.name</code></pre>
-<p>shows:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> soma</code></pre>
-<p>The <code>Compartment</code> elements model small portions of a neuron. Some basic experiments can be carried out using a single compartment. Let us create another object to act on the <code>soma</code>. This will be a step current generator to inject a current pulse into the soma.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> pulse = moose.PulseGen(<span class="st">'/model/pulse'</span>)</code></pre>
-<p>You can use <code>le</code> at any point to see what is there:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.le(<span class="st">'/model'</span>)</code></pre>
-<p>will show you:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> Elements under /model
- /model/soma
- /model/pulse</code></pre>
-<p>And finally, we can create a <code>Table</code> to record the time series of the soma's membrane potential. It is good practice to organize the data separately from the model. So we do it as below:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> data = moose.Neutral(<span class="st">'/data'</span>)
- vmtab = moose.Table(<span class="st">'/data/soma_Vm'</span>)</code></pre>
-<p>Now that we have the essential elements for a small model, we can go on to set the properties of this model and the experimental protocol.</p>
-<h1 id="setting-the-properties-of-elements-accessing-fields"><a href="#setting-the-properties-of-elements-accessing-fields">Setting the properties of elements: accessing fields</a></h1>
-<p>Elements have several kinds of fields. The simplest ones are the <code>value fields</code>. These can be accessed like ordinary Python members. You can list the available value fields using <code>getFieldNames</code> function:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> soma.getFieldNames(<span class="st">'valueFinfo'</span>)</code></pre>
-<p>Here <code>valueFinfo</code> is the type name for value fields. <code>Finfo</code> is short form of <em>field information</em>. For each type of field there is a name ending with <code>-Finfo</code>. The above will display the following list:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> (<span class="st">'this'</span>,
- <span class="co">'name'</span>,
- <span class="co">'me'</span>,
- <span class="co">'parent'</span>,
- <span class="co">'children'</span>,
- <span class="co">'path'</span>,
- <span class="co">'class'</span>,
- <span class="co">'linearSize'</span>,
- <span class="co">'objectDimensions'</span>,
- <span class="co">'lastDimension'</span>,
- <span class="co">'localNumField'</span>,
- <span class="co">'pathIndices'</span>,
- <span class="co">'msgOut'</span>,
- <span class="co">'msgIn'</span>,
- <span class="co">'Vm'</span>,
- <span class="co">'Cm'</span>,
- <span class="co">'Em'</span>,
- <span class="co">'Im'</span>,
- <span class="co">'inject'</span>,
- <span class="co">'initVm'</span>,
- <span class="co">'Rm'</span>,
- <span class="co">'Ra'</span>,
- <span class="co">'diameter'</span>,
- <span class="co">'length'</span>,
- <span class="co">'x0'</span>,
- <span class="co">'y0'</span>,
- <span class="co">'z0'</span>,
- <span class="co">'x'</span>,
- <span class="co">'y'</span>,
- <span class="co">'z'</span>)</code></pre>
-<p>Some of these fields are for internal or advanced use, some give access to the physical properties of the biological entity we are trying to model. Now we are interested in <code>Cm</code>, <code>Rm</code>, <code>Em</code> and <code>initVm</code>. In the most basic form, a neuronal compartment acts like a parallel <code>RC</code> circuit with a battery attached. Here <code>R</code> and <code>C</code> are resistor and capacitor connected in parallel, and the battery with voltage <code>Em</code> is in series with the resistor, as shown below:</p>
-<hr />
-<div class="figure">
-<img src="../../images/neuronalcompartment.jpg" alt="Passive neuronal compartment" /><p class="caption"><strong>Passive neuronal compartment</strong></p>
-</div>
-<hr />
-<p>The fields are populated with some defaults.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.Cm, soma.Rm, soma.Vm, soma.Em, soma.initVm</code></pre>
-<p>will give you:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="fl">1.0</span> <span class="fl">1.0</span> -<span class="fl">0.06</span> -<span class="fl">0.06</span> -<span class="fl">0.06</span></code></pre>
-<p>You can set the <code>Cm</code> and <code>Rm</code> fields to something realistic using simple assignment (we follow SI unit)<a href="#fn2" class="footnoteRef" id="fnref2"><sup>2</sup></a>.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> soma.Cm = <span class="fl">1e-9</span>
- soma.Rm = <span class="fl">1e7</span>
- soma.initVm = -<span class="fl">0.07</span></code></pre>
-<p>Instead of writing print statements for each field, you could use the utility function showfield to see that the changes took effect:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.showfield(soma)</code></pre>
-<p>will list most of the fields with their values:</p>
-<p><sub><sub><del>{.c} [ /model/soma ] diameter = 0.0 linearSize = 1 localNumField = 0 Ra = 1.0 y0 = 0.0 Rm = 10000000.0 inject = 0.0 Em = -0.06 initVm = -0.07 x = 0.0 path = /model/soma x0 = 0.0 z0 = 0.0 class = Compartment name = soma Cm = 1e-09 Vm = -0.06 length = 0.0 Im = 0.0 y = 0.0 lastDimension = 0 z = 0.0</del></sub></sub>{.python}</p>
-<p>Now we can setup the current pulse to be delivered to the soma:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> pulse.delay[<span class="dv">0</span>] = <span class="fl">50e-3</span>
- pulse.width[<span class="dv">0</span>] = <span class="fl">100e-3</span>
- pulse.level[<span class="dv">0</span>] = <span class="fl">1e-9</span>
- pulse.delay[<span class="dv">1</span>] = <span class="fl">1e9</span></code></pre>
-<p>This tells the pulse generator to create a 100 ms long pulse 50 ms after the start of the simulation. The amplitude of the pulse is set to 1 nA. We set the delay for the next pulse to a very large value (larger than the total simulation time) so that the stimulation stops after the first pulse. Had we set <code>pulse.delay = 0</code> , it would have generated a pulse train at 50 ms intervals.</p>
-<h1 id="putting-them-together-setting-up-connections"><a href="#putting-them-together-setting-up-connections">Putting them together: setting up connections</a></h1>
-<p>In order for the elements to interact during simulation, we need to connect them via messages. Elements are connected to each other using special source and destination fields. These types are named <code>srcFinfo</code> and <code>destFinfo</code>. You can query the available source and destination fields on an element using <code>getFieldNames</code> as before. This time, let us do it another way: by the class name:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.getFieldNames(<span class="st">'PulseGen'</span>, <span class="st">'srcFinfo'</span>)</code></pre>
-<p>This form has the advantage that you can get information about a class without creating elements of that class. The above code shows:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> (<span class="st">'childMsg'</span>, <span class="st">'outputOut'</span>)</code></pre>
-<p>Here <code>childMsg</code> is a source field that is used by the MOOSE internals to connect child elements to parent elements. The second one is of our interest. Check out the built-in documentation here:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.doc(<span class="st">'PulseGen.outputOut'</span>)</code></pre>
-<p>shows:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> PulseGen.outputOut: double - source field
- Current output level.</code></pre>
-<p>so this is the output of the pulse generator and this must be injected into the <code>soma</code> to stimulate it. But where in the <code>soma</code> can we send it? Again, MOOSE has some introspection built in.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> soma.getFieldNames(<span class="st">'destFinfo'</span>)</code></pre>
-<p>shows:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> (<span class="st">'parentMsg'</span>,
- <span class="co">'set_this'</span>,
- <span class="co">'get_this'</span>,
- ...
- <span class="co">'set_z'</span>,
- <span class="co">'get_z'</span>,
- <span class="co">'injectMsg'</span>,
- <span class="co">'randInject'</span>,
- <span class="co">'cable'</span>,
- <span class="co">'process'</span>,
- <span class="co">'reinit'</span>,
- <span class="co">'initProc'</span>,
- <span class="co">'initReinit'</span>,
- <span class="co">'handleChannel'</span>,
- <span class="co">'handleRaxial'</span>,
- <span class="co">'handleAxial'</span>)</code></pre>
-<p>Now that is a long list. But much of it are fields for internal or special use. Anything that starts with <code>get_</code> or <code>set_</code> are internal <code>destFinfo</code> used for accessing value fields (we shall use one of those when setting up data recording). Among the rest <code>injectMsg</code> seems to be the most likely candidate. Use the <code>connect</code> function to connect the pulse generator output to the soma input:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> m = moose.<span class="ot">connect</span>(pulse, <span class="st">'outputOut'</span>, soma, <span class="st">'injectMsg'</span>)</code></pre>
-<p><code>connect(source, source_field, dest, dest_field)</code> creates a <code>message</code> from <code>source</code> element's <code>source_field</code> field to <code>dest</code> elements <code>dest_field</code> field and returns that message. Messages are also elements. You can print them to see their identity:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> m</code></pre>
-<p>on my system gives:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <moose.SingleMsg: <span class="dt">id</span>=<span class="dv">5</span>, dataId=<span class="dv">733</span>, path=/Msgs/singleMsg[<span class="dv">733</span>]></code></pre>
-<p>You can print any element as above and the string representation will show you the class, two numbers(<code>id</code> and <code>dataId</code>) uniquely identifying it among all elements, and its path. You can get some more information about a message:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> m.e1.path, m.e2.path, m.srcFieldsOnE1, m.destFieldsOnE2</code></pre>
-<p>will confirm what you already know:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> /model/pulse /model/soma (<span class="st">'outputOut'</span>,) (<span class="st">'injectMsg'</span>,)</code></pre>
-<p>A message element has fields <code>e1</code> and <code>e2</code> referring to the elements it connects. For single one-directional messages these are source and destination elements, which are <code>pulse</code> and <code>soma</code> respectively. The next two items are lists of the field names which are connected by this message.</p>
-<p>You could also check which elements are connected to a particular field:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.neighbours[<span class="st">'injectMsg'</span>]</code></pre>
-<p>shows:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> [<moose.ematrix: <span class="kw">class</span>=PulseGen, <span class="dt">id</span>=<span class="dv">729</span>,path=/model/pulse>]</code></pre>
-<p>Notice that the list contains something called ematrix. We discuss this <a href="#some-more-details">later</a>. Also <code>neighbours</code> is a new kind of field: <code>lookupFinfo</code> which behaves like a dictionary. Next we connect the table to the soma to retrieve its membrane potential <code>Vm</code>. This is where all those <code>destFinfo</code> starting with <code>get_</code> or <code>set_</code> come in use. For each value field <code>X</code>, there is a <code>destFinfo</code> <code>get_{X}</code> to retrieve the value at simulation time. This is used by the table to record the values <code>Vm</code> takes.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.<span class="ot">connect</span>(vmtab, <span class="st">'requestData'</span>, soma, <span class="st">'get_Vm'</span>)</code></pre>
-<p>This finishes our model and recording setup. You might be wondering about the source-destination relationship above. It is natural to think that <code>soma</code> is the source of <code>Vm</code> values which should be sent to <code>vmtab</code>. But here <code>requestData</code> is a <code>srcFinfo</code> acting like a reply card. This mode of obtaining data is called <em>pull</em> mode.<a href="#fn3" class="footnoteRef" id="fnref3"><sup>3</sup></a></p>
-<h1 id="scheduling-and-running-the-simulation"><a href="#scheduling-and-running-the-simulation">Scheduling and running the simulation</a></h1>
-<p>With the model all set up, we have to schedule the simulation. MOOSE has a central clock element (<code>/clock</code>) to manage time. Clock has a set of <code>Tick</code> elements under it that take care of advancing the state of each element with time as the simulation progresses. Every element to be included in a simulation must be assigned a tick. Each tick can have a different ticking interval (<code>dt</code>) that allows different elements to be updated at different rates. We initialize the ticks and set their <code>dt</code> values using the <code>setClock</code> function.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.setClock(<span class="dv">0</span>, <span class="fl">0.025e-3</span>)
- moose.setClock(<span class="dv">1</span>, <span class="fl">0.025e-3</span>)
- moose.setClock(<span class="dv">2</span>, <span class="fl">0.25e-3</span>)</code></pre>
-<p>This will initialize tick #0 and tick #1 with <code>dt = 25</code> μs and tick #2 with <code>dt = 250</code> μs. Thus all the elements scheduled on ticks #0 and 1 will be updated every 25 μs and those on tick #2 every 250 μs. We use the faster clocks for the model components where finer timescale is required for numerical accuracy and the slower clock to sample the values of <code>Vm</code>.</p>
-<p>So to assign tick #2 to the table for recording <code>Vm</code>, we pass its whole path to the <code>useClock</code> function.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.useClock(<span class="dv">2</span>, <span class="st">'/data/soma_Vm'</span>, <span class="st">'process'</span>)</code></pre>
-<p>Read this as "use tick # 2 on the element at path <code>/data/soma_Vm</code> to call its <code>process</code> method at every step". Every class that is supposed to update its state or take some action during simulation implements a <code>process</code> method. And in most cases that is the method we want the ticks to call at every time step. A less common method is <code>init</code>, which is implemented in some classes to interleave actions or updates that must be executed in a specific order<a href="#fn4" class="footnoteRef" id="fnref4"><sup>4</sup></a>. The <code>Compartment</code> class is one such case where a neuronal compartment has to know the <code>Vm</code> of its neighboring compartments before it can calculate its <code>Vm</code> for the next step. This is done with:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.useClock(<span class="dv">0</span>, soma.path, <span class="st">'init'</span>)</code></pre>
-<p>Here we used the <code>path</code> field instead of writing the path explicitly.</p>
-<p>Next we assign tick #1 to process method of everything under <code>/model</code>.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.useClock(<span class="dv">1</span>, <span class="st">'/model/##'</span>, <span class="st">'process'</span>)</code></pre>
-<p>Here the second argument is an example of wild-card path. The <code>##</code> matches everything under the path preceding it at any depth. Thus if we had some other objects under <code>/model/soma</code>, <code>process</code> method of those would also have been scheduled on tick #1. This is very useful for complex models where it is tedious to scheduled each element individually. In this case we could have used <code>/model/#</code> as well for the path. This is a single level wild-card which matches only the children of <code>/model</code> but does not go farther down in the hierarchy.</p>
-<p>Once the elements are assigned ticks, we can put the model to its initial state using:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.reinit()</code></pre>
-<p>You may remember that we had changed initVm from <code>-0.06</code> to <code>-0.07</code>. The reinit call we initialize <code>Vm</code> to that value. You can verify that:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> soma.Vm</code></pre>
-<p>gives:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> -<span class="fl">0.07</span></code></pre>
-<p>Finally, we run the simulation for 300 ms:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> moose.start(<span class="fl">300e-3</span>)</code></pre>
-<p>The data will be recorded by the <code>soma_vm</code> table, which is referenced by the variable <code>vmtab</code>. The <code>Table</code> class provides a numpy array interface to its content. The field is <code>vec</code>. So you can easily plot the membrane potential using the <a href="http://matplotlib.org/">matplotlib</a> library.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="ch">import</span> pylab
- t = pylab.linspace(<span class="dv">0</span>, <span class="fl">300e-3</span>, <span class="dt">len</span>(vmtab.vec))
- pylab.plot(t, vmtab.vec)
- pylab.show()</code></pre>
-<p>The first line imports the pylab submodule from matplotlib. This useful for interactive plotting. The second line creates the time points to match our simulation time and length of the recorded data. The third line plots the <code>Vm</code> and the fourth line makes it visible. Does the plot match your expectation?</p>
-<h1 id="some-more-details"><a href="#some-more-details">Some more details</a></h1>
-<h2 id="ematrix-melement-and-element"><a href="#ematrix-melement-and-element"><code>ematrix</code>, <code>melement</code> and <code>element</code></a></h2>
-<p>MOOSE elements are instances of the class <code>melement</code>. <code>Compartment</code>, <code>PulseGen</code> and other MOOSE classes are derived classes of <code>melement</code>. All <code>melement</code> instances are contained in array-like structures called <code>ematrix</code>. Each <code>ematrix</code> object has a numerical <code>id_</code> field uniquely identifying it. An <code>ematrix</code> can have one or more elements. You can create an array of elements:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> comp_array = moose.ematrix(<span class="st">'/model/comp'</span>, (<span class="dv">3</span>,), <span class="st">'Compartment'</span>)</code></pre>
-<p>This tells MOOSE to create an <code>ematrix</code> of 3 <code>Compartment</code> elements with path <code>/model/comp</code>. For <code>ematrix</code> objects with multiple elements, the index in the <code>ematrix</code> is part of the element path.</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="dt">print</span> comp_array.path, <span class="dt">type</span>(comp_array)</code></pre>
-<p>shows that <code>comp_array</code> is an instance of <code>ematrix</code> class. You can loop through the elements in an <code>ematrix</code> like a Python list:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> <span class="kw">for</span> comp in comp_array:
- <span class="dt">print</span> comp.path, <span class="dt">type</span>(comp)</code></pre>
-<p>shows:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> /model/comp[<span class="dv">0</span>] <<span class="dt">type</span> <span class="st">'moose.melement'</span>>
- /model/comp[<span class="dv">1</span>] <<span class="dt">type</span> <span class="st">'moose.melement'</span>>
- /model/comp[<span class="dv">2</span>] <<span class="dt">type</span> <span class="st">'moose.melement'</span>></code></pre>
-<p>Thus elements are instances of class <code>melement</code>. All elements in an <code>ematrix</code> share the <code>id_</code> of the <code>ematrix</code> which can retrieved by <code>melement.getId()</code>.</p>
-<p>A frequent use case is that after loading a model from a file one knows the paths of various model components but does not know the appropriate class name for them. For this scenario there is a function called <code>element</code> which converts ("casts" in programming jargon) a path or any moose object to its proper MOOSE class. You can create additional references to <code>soma</code> in the example this way:</p>
-<pre class="sourceCode python"><code class="sourceCode python"> x = moose.element(<span class="st">'/model/soma'</span>)</code></pre>
-<p>Any MOOSE class can be extended in Python. But any additional attributes added in Python are invisible to MOOSE. So those can be used for functionalities at the Python level only. You can see <code>Demos/squid/squid.py</code> for an example.</p>
-<h2 id="finfos"><a href="#finfos"><code>Finfos</code></a></h2>
-<p>The following kinds of <code>Finfo</code> are accessible in Python</p>
-<ul>
-<li><strong><code>valueFinfo</code></strong> : simple values. For each readable <code>valueFinfo</code> <code>XYZ</code> there is a <code>destFinfo</code> <code>get_XYZ</code> that can be used for reading the value at run time. If <code>XYZ</code> is writable then there will also be <code>destFinfo</code> to set it: <code>set_XYZ</code>. Example: <code>Compartment.Rm</code></li>
-<li><strong><code>lookupFinfo</code></strong> : lookup tables. These fields act like Python dictionaries but iteration is not supported. Example: <code>Neutral.neighbours</code>.</li>
-<li><strong><code>srcFinfo</code></strong> : source of a message. Example: <code>PulseGen.outputOut</code>.</li>
-<li><strong><code>destFinfo</code></strong> : destination of a message. Example: <code>Compartment.injectMsg</code>. Apart from being used in setting up messages, these are accessible as functions from Python. <code>HHGate.setupAlpha</code> is an example.</li>
-<li><strong><code>sharedFinfo</code></strong> : a composition of source and destination fields. Example: <code>Compartment.channel</code>.</li>
-</ul>
-<h1 id="moving-on"><a href="#moving-on">Moving on</a></h1>
-<p>Now you know the basics of pymoose and how to access the help system. MOOSE is backward compatible with GENESIS and most GENESIS classes have been reimplemented in MOOSE. There is slight change in naming (MOOSE uses CamelCase), and setting up messages are different. But <a href="http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual.html">GENESIS documentation</a> is still a good source for documentation on classes that have been ported from GENESIS.</p>
-<p>In addition, the <code>Demos/snippets</code> directory in your MOOSE installation has small executable python scripts that show usage of specific classes or functionalities. Beyond that you can browse the code in the <code>Demos</code> directory to see some more complex models.</p>
-<p>If the built-in MOOSE classes do not satisfy your needs entirely, you are welcome to add new classes to MOOSE. The API documentation will help you get started. Finally you can join the <a href="https://lists.sourceforge.net/lists/listinfo/moose-generic">moose mailing list</a> and request for help.</p>
-<div class="footnotes">
-<hr />
-<ol>
-<li id="fn1"><p>To list the classes only, use <code>moose.le('/classes')</code><a href="#fnref1">↩</a></p></li>
-<li id="fn2"><p>MOOSE is unit agnostic and things should work fine as long as you use values all converted to a consistent unit system.<a href="#fnref2">↩</a></p></li>
-<li id="fn3"><p>This apparently convoluted implementation is for performance reason. Can you figure out why? <em>Hint: the table is driven by a slower clock than the compartment.</em><a href="#fnref3">↩</a></p></li>
-<li id="fn4"><p>In principle any function available in a MOOSE class can be executed periodically this way as long as that class exposes the function for scheduling following the MOOSE API. So you have to consult the class' documentation for any nonstandard methods that can be scheduled this way.<a href="#fnref4">↩</a></p></li>
-</ol>
-</div>
-</body>
-</html>
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Style-Type" content="text/css" />
- <meta name="generator" content="pandoc" />
- <meta name="author" content="Niraj Dudani" />
- <title>User documentation for MOOSE</title>
- <style type="text/css">code{white-space: pre;}</style>
- <link rel="stylesheet" href="html/css/moosedocs.css" type="text/css" />
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-<body>
-<div id="header">
-<h1 class="title">User documentation for MOOSE</h1>
-<h2 class="author">Niraj Dudani</h2>
-<h3 class="date">January 1, 2013</h3>
-</div>
-<h2 id="index-for-all-documents">Index for all documents</h2>
-<ul>
-<li><a href="html/pymoose2walkthrough.html">Getting started with python scripting for MOOSE</a></li>
-<li><a href="html/MooseGuiDocs.html">MOOSEGUI: Graphical interface for MOOSE</a></li>
-<li><a href="html/Nkit2Documentation.html">Neuronal simulations in MOOSEGUI</a></li>
-<li><a href="html/Kkit12Documentation.html">Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI</a></li>
-<li><a href="html/moosebuiltindocs.html">Documentation for all MOOSE classes and functions</a></li>
-</ul>
-</body>
-</html>
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------
-
-# Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI
-
-Upinder Bhalla, Harsha Rani
-
-Sep 5 2013.
-
------
-
-* [Introduction](#introduction)
-
-* [**TODO** What are chemical kinetic models?](#todo-what-are-chemical-kinetic-models)
- * [Levels of model](#levels-of-model)
- * [Numerical methods](#numerical-methods)
-* [Using Kinetikit 12](#using-kinetikit-12)
-
- * [Overview](#overview)
- * [Model layout and icons](#model-layout-and-icons)
-
- * [Compartment](#compartment)
- * [Pool](#pool)
- * [Buffered pools](#buffered-pools)
- * [Reaction](#reaction)
- * [Mass-action enzymes](#mass-action-enzymes)
- * [Michaelis-Menten Enzymes](#michaelis-menten-enzymes)
- * [Function](#function)
- * [Model operations](#model-operations)
- * [Model Building](#model-building)
-
-## [Introduction](#TOC)
-
-Kinetikit 12 is a graphical interface for doing chemical kinetic modeling in MOOSE. It is derived in part from Kinetikit, which was the graphical interface used in GENESIS for similar models. Kinetikit, also known as kkit, was at version 11 with GENESIS. Here we start with Kinetikit 12.
-
-## [**TODO** What are chemical kinetic models?](#TOC)
-
-Much of neuronal computation occurs through chemical signaling. For example, many forms of synaptic plasticity begin with calcium influx into the synapse, followed by calcium binding to calmodulin, and then calmodulin activation of numerous enzymes. These events can be represented in chemical terms:
-
-> 4 Ca<sup>2+</sup> + CaM <===> Ca<sub>4</sub>.CaM
-
-Such chemical equations can be modeled through standard Ordinary Differential Equations, if we ignore space:
-
-> d[Ca]/dt = −4K<sub>f</sub> ∗ [Ca]<sup>4</sup> ∗ [CaM] + 4K<sub>b</sub> ∗ [Ca<sub>4</sub>.CaM]
-> d[CaM]/dt = −K<sub>f</sub> ∗ [Ca]<sup>4</sup> ∗ [CaM] + K<sub>b</sub> ∗ [Ca<sub>4</sub>.CaM]
-> d[Ca4.CaM]/dt = K<sub>f</sub> ∗ [Ca]<sup>4</sup> ∗ [CaM] − K<sub>b</sub> ∗ [Ca<sub>4</sub>.CaM]
-
-MOOSE models these chemical systems. This help document describes how to do such modelling using the graphical interface, Kinetikit 12.
-
-### [Levels of model](#TOC)
-
-Chemical kinetic models can be simple well-stirred (or point) models, or they could have multiple interacting compartments, or they could include space explicitly using reaction-diffusion. In addition such models could be solved either deterministically, or using a stochastic formulation. At present Kinetikit handles compartmental models but does not compute diffusion within the compartments, though MOOSE itself can do this at the script level. Kkit12 will do deterministic as well as stochastic chemical calculations.
-
-### [Numerical methods](#TOC)
-
-* **Deterministic**: Adaptive timestep 5th order Runge-Kutta-Fehlberg from the GSL (GNU Scientific Library).
-* **Stochastic**: Optimized Gillespie Stochastic Systems Algorithm, custom implementation.
-
-## [Using Kinetikit 12](#TOC)
-
-### [Overview](#TOC)
-
-* Load models using **`File -> Load model`**. A reaction schematic for the chemical system appears in the **`Editor view`** tab.
-* View parameters in **`Editor view`** tab by clicking on icons, and looking at entries in **`Properties`** table to the right.
-* Edit parameters by changing their values in the **`Properties`** table.
-* From Run View, Pools can be plotted by clicking on their icons and dragging the icons onto the plot Window. Presently only concentration is plottable.
-* Run models using **`Run`** button.
-* Select numerical method using options under **`Preferences`** button in simulation control.
-
-<!--* Save plots using the icons at the bottom of the **`Plot Window`**.
-
-Most of these operations are detailed in other sections, and are shared with other aspects of the MOOSE simulation interface. Here we focus on the Kinetikit-specific items.
-
-### [Model layout and icons](#TOC)
-
-When you are in the **`Model View`** tab you will see a collection of icons, arrows, and grey boxes surrounding these. This is a schematic of the reaction scheme being modeled. You can view and change parameters, and change the layout of the model.
-
-
-
-
-Resizing the model layout and icons:
-
-* **Zoom**: Comma and period keys. Alternatively, the mouse scroll wheel or vertical scroll line on the track pad will cause the display to zoom in and out.
-* **Pan**: The arrow keys move the display left, right, up, and down.
-* **Entire Model View**: Pressing the **`a`** key will fit the entire model into the entire field of view.
-* **Resize Icons**: Angle bracket keys, that is, **`<`** and **`>`** or **`+`** and **`-`**. This resizes the icons while leaving their positions on the screen layout more or less the same.
-* **Original Model View**: Presing the **`A`** key (capital `A`) will revert to the original model view including the original icon scaling.
-
-#### [Compartment](#TOC)
-
-The _compartment_ in moose is usually a contiguous domain in which a certain set of chemical reactions and molecular species occur. The definition is very closely related to that of a cell-biological compartment. Examples include the extracellular space, the cell membrane, the cytosol, and the nucleus. Compartments can be nested, but of course you cannot put a bigger compartment into a smaller one.
-
-* **Icon**: Grey boundary around a set of reactions.
-* **Moving Compartments**: Click and drag on the boundary.
-* **Resizing Compartment boundary**: Happens automatically when contents are repositioned, so that the boundary just contains contents.
-* **Compartment editable parameters**:
-
- * **`name`**: The name of the compartment.
- * **`size`**: This is the volume, surface area or length of the compartment, depending on its type.
-* **Compartment fixed parameters**:
-
- * **`numDimensions`**: This specifies whether the compartment is a volume, a 2-D surface, or if it is just being represented as a length.
-
-#### [Pool](#TOC)
-
-This is the set of molecules of a given species within a compartment. Different chemical states of the same molecule are in different pools.
-
-* **Icon**:  Colored rectangle with pool name in it.
-* **Moving pools**: Click and drag.
-* **Pool editable parameters**:
-
- * **`name`**: Name of the pool
- * **`n`**: Number of molecules in the pool
- * **`nInit`**: Initial number of molecules in the pool. `n` gets set to this value when the `reinit` operation is done.
- * **`conc`**: Concentration of the molecules in the pool.
-
- > conc = n * unit_scale_factor / (N<sub>A</sub> * vol)
- * **`concInit`**: Initial concentration of the molecules in the pool.
-
- > concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol)
-`conc` is set to this value when the `reinit` operation is done.
-* **Pool fixed parameters**
-
- * **`size`**: Derived from the compartment that holds the pool. Specifies volume, surface area or length of the holding compartment.
-
-#### [Buffered pools](#TOC)
-
-Some pools are set to a fixed `n`, that is number of molecules, and therefore a fixed concentration, throughout a simulation. These are buffered pools.
-
-* **Icon**:  Colored rectangle with pool name in it.
-* **Moving Buffered pools**: Click and drag.
-* **Buffered Pool editable parameters**
-
- * **`name`**: Name of the pool
- * **`nInit`**: Fixed number of molecules in the pool. `n` gets set to this value throughout the run.
- * **`concInit`**: Fixed concentration of the molecules in the pool.
-
- > concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol)
-`conc` is set to this value throughout the run.
-* **Pool fixed parameters**:
-
- * **`n`**: Number of molecules in the pool. Derived from `nInit`.
- * **`conc`**: Concentration of molecules in the pool. Derived from `concInit`.
- * **`size`**: Derived from the compartment that holds the pool. Specifies volume, surface area or length of the holding compartment.
-
-#### [Reaction](#TOC)
-
-These are conversion reactions between sets of pools. They are reversible, but you can set either of the rates to zero to get irreversibility. In the illustration below, **`D`** and **`A`** are substrates, and **`B`** is the product of the reaction. This is indicated by the direction of the green arrow.
-
-
-
-
-* **Icon**:  Reversible reaction arrow.
-* **Moving Reactions**: Click and drag.
-* **Reaction editable parameters**:
-
- * name : Name of reaction
- * K~f~ : Forward rate of reaction, in `concentration/time` units. This is the normal way to express and manipulate the reaction rate.
- * k~f~ : Forward rate of reaction, in `number/time` units. This is used internally for computations, but is volume-dependent and should not be used to manipulate the reaction rate unless you really know what you are doing.
- * K~b~ : Backward rate of reaction, in `concentration/time` units. This is the normal way to express and manipulate the reaction rate.
- * k~b~ : Backward rate of reaction, in `number/time` units. This is used internally for computations, but is volume-dependent and should not be used to manipulate the reaction rate unless you really know what you are doing.
-* **Reaction fixed parameters**:
-
- * **numProducts**: Number of product molecules.
- * **numSubstrates**: Number of substrates molecules.
-
-#### [Mass-action enzymes](#TOC)
-
-These are enzymes that model the chemical equations
-
-> E + S <===> E.S -> E + P
-
-Note that the second reaction is irreversible. Note also that mass-action enzymes include a pool to represent the **`E.S`** (enzyme-substrate) complex. In the example below, the enzyme pool is named **`MassActionEnz`**, the substrate is **`C`**, and the product is **`E`**. The direction of the enzyme reaction is indicated by the red arrows.
-
-
-
-
-
-* **Icon**:  Colored ellipse atop a small square. The ellipse represents the enzyme. The small square represents **`E.S`**, the enzyme-substrate complex. The ellipse icon has the same color as the enzyme pool **`E`**. It is connected to the enzyme pool **`E`** with a straight line of the same color.
-
- The ellipse icon sits on a continuous, typically curved arrow in red, from the substrate to the product.
-
- A given enzyme pool can have any number of enzyme activities, since the same enzyme might catalyze many reactions.
-
-* **Moving Enzymes**: Click and drag on the ellipse.
-* **Enzyme editable parameters**
-
- * name : Name of enzyme.
- * K~m~ : Michaelis-Menten value for enzyme, in `concentration` units.
- * k~cat~ : Production rate of enzyme, in `1/time` units. Equal to k~3~, the rate of the second, irreversible reaction.
- * k~1~ : Forward rate of the **E+S** reaction, in number and `1/time` units. This is what is used in the internal calculations.
- * k~2~: Backward rate of the **E+S** reaction, in `1/time` units. Used in internal calculations.
- * k~3~: Forward rate of the **E.S -> E + P** reaction, in `1/time` units. Equivalent to k~cat~. Used in internal calculations.
- * ratio: This is equal to k~2~/k~3~. Needed to define the internal rates in terms of K~m~ and k~cat~. I usually use a value of 4.
-* **Enzyme-substrate-complex editable parameters**: These are identical to those of any other pool.
-
- * **name**: Name of the **`E.S`** complex. Defaults to **`<enzymeName>_cplx`**.
- * **n**: Number of molecules in the pool
- * **nInit**: Initial number of molecules in the complex. `n` gets set to this value when the `reinit` operation is done.
- * **conc**: Concentration of the molecules in the pool.
-
- > conc = n * unit_scale_factor / (N<sub>A</sub> * vol)
- * **`concInit`**: Initial concentration of the molecules in the pool.
-
- > concInit = nInit * unit_scale_factor / (N<sub>A</sub> * vol)
-`conc` is set to this value when the `reinit` operation is done.
-* **Enzyme-substrate-complex fixed parameters**:
-
- * **size**: Derived from the compartment that holds the pool. Specifies volume, surface area or length of the holding compartment. Note that the Enzyme-substrate-complex is assumed to be in the same compartment as the enzyme molecule.
-
-#### [Michaelis-Menten Enzymes](#TOC)
-
-These are enzymes that obey the Michaelis-Menten equation
-
-> V = V<sub>max</sub> * [S] / ( K<sub>m</sub> + [S] ) = k<sub>cat</sub> * [Etot] * [S] / ( K<sub>m</sub> + [S] )
-
-where
-
-* V~max~ is the maximum rate of the enzyme
-* [Etot] is the total amount of the enzyme
-* K~m~ is the Michaelis-Menten constant
-* S is the substrate.
-
-Nominally these enzymes model the same chemical equation as the mass-action enzyme:
-
-> E + S <===> E.S -> E + P
-
-but they make the assumption that the **``E.S``** is in a quasi-steady-state with **``E``** and **``S``**, and they also ignore sequestration of the enzyme into the complex. So there is no representation of the **``E.S``** complex. In the example below, the enzyme pool is named **``MM_Enz``**, the substrate is **``E``**, and the product is **``F``**. The direction of the enzyme reaction is indicated by the red arrows.
-
-
-
-
-* **Icon**:  Colored ellipse. The ellipse represents the enzyme The ellipse icon has the same color as the enzyme **`MM_Enz`**. It is connected to the enzyme pool **`MM_Enz`** with a straight line of the same color. The ellipse icon sits on a continuous, typically curved arrow in red, from the substrate to the product. A given enzyme pool can have any number of enzyme activities, since the same enzyme might catalyze many reactions.
-* **Moving Enzymes**: Click and drag.
-* **Enzyme editable parameters**:
-
- * name: Name of enzyme.
- * K~m~: Michaelis-Menten value for enzyme, in `concentration` units.
- * k~cat~: Production rate of enzyme, in `1/time` units. Equal to k~3~, the rate of the second, irreversible reaction.
-
-#### [Function](#TOC)
-
-Function objects can be used to evaluate expressions with arbitrary number of variables and constants. We can assign expression of the form:
-
-f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP )
-
-where ci‘s are constants and xi‘s and yi‘s are variables.
-
-It can parse mathematical expression defining a function and evaluate it and/or its derivative for specified variable values. The variables can be input from other moose objects. In case of arbitrary variable names, the source message must have the variable name as the first argument.
-
-* **Icon**: Colored rectangle with pool name. This is **`Æ’`** in the example image below. The input pools **`A`** and **`B`** connect to the **ƒ** with blue arrows. The function ouput's to BuffPool
-
-### [Model operations](#TOC)
-
-* **Loading models**: **`File -> Load Model -> select from dialog`**. This operation makes the previously loaded model disable and loads newly selected models in **`Model View`**
-* **New**: **`File -> New -> Model name `**. This opens a empty widget for model building
-* **Saving models**: **`File -> Save Model -> select from dialog`**.
-* **Changing numerical methods**: **`Preference->Chemical tab`** item from Simulation Control. Currently supports:
-
- * Runge Kutta: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions.
- * Gillespie: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up.
- * Exponential Euler:This methods computes the solution of partial and ordinary differential equations.
-
-### [Model building](#TOC)
-
-
-
-* The Edit Widget includes various menu options and model icons on the top.* Use the mouse buttton to click and drag icons from toolbar to Edit Widget, two things will happen, icon will appear in the editor widget
- and a object editor will pop up with lots of parameters with respect to moose object.
-Rules:
-
- * Compartment has to be created firstly \n(At present only single compartment model is allowed)
- * Enzyme should be dropped on a pool as parent and function should be dropped on buffPool for output
- <li> Drag in pool's and reaction on to the editor widget, now one can set up a reaction.Click on mooseObject one can find a little arrow on the top right corner of the object, drag from this little arrow to any object for connection.E.g pool to reaction and reaction to pool. Specific connection type gets specific colored arrow. E.g. Green color arrow for specifying connection between reactant and product for reaction.
-Clicking on the object one can rearrange object for clean layout.
-Second order reaction can also be done by repeating the connection over again
-* Each connection can be deleted and using rubberband selection each moose object can be deleted
-
-
-
-* From run widget, pools are draggable to plot window for plotting. (Currently **`conc`** is plotted as default field)
- Plots are color-coded as per in model.
-* Model can be run by clicking start button. One can stop button in mid-stream and start up again without affectiong the calculations.
- The reset button clears the simulation.
diff --git a/moose-core/Docs/user/markdown/MooseGuiDocs.markdown b/moose-core/Docs/user/markdown/MooseGuiDocs.markdown
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------
-
-# **MOOSE GUI: Graphical interface for MOOSE**
-
-Upinder Bhalla, Harsha Rani, Aviral Goel
-
-Aug 28 2013.
-
------
-
-## Contents
-- [Introduction](#introduction)
-- [Interface](#interface)
- * [Menu Bar](#menu-bar)
- * [File](#menu-file)
- * [New](#file-new)
- * [Load Model](#file-load-model)
- * [Connect BioModels](#file-connect-biomodels)
- * [Quit](#file-quit)
- * [View](#menu-view)
- * [Editor View](#editor-view)
- * [Run View](#run-view)
- * [Dock Widgets](#dock-widgets)
- * [SubWindows](#subwindows)
- * [Help](#menu-help)
- * [About MOOSE](#about-moose)
- * [Built-in Documentation](#built-in-documentation)
- * [Report a bug](#report-a-bug)
- * [Editor View](#editor-view)
- * [Model Editor](#model-editor)
- * [Property Editor](#property-editor)
- * [Run View](#run-view)
- * [Simulation Controls](#simulation-controls)
- * [Plot Widget](#plot-widget)
- * [Toolbar](#plot-widget-toolbar)
- * [Context Menu](#plot-widget-context-menu)
-
-## Introduction
-
-The Moose GUI currently allow you work on [chemical](Kkit12Documentation.html) models using a interface. This document describes the salient features of the GUI
-
-## Interface
-
- The interface layout consists of a [menu bar](#menu-bar) and two views, [editor view](#editor-view) and [run view](#run-view).
-
-### Menu Bar
-
-
-
-The menu bar appears at the top of the main window. In Ubuntu 12.04, the menu bar appears only when the mouse is in the top menu strip of the screen. It consists of the following options -
-
-#### File
-
-The File menu option provides the following sub options -
-
-- [New](#file-new) - Create a new chemical signalling model.
-- [Load Model](#file-load-model) - Load a chemical signalling or compartmental neuronal model from a file.
-- [Paper_2015_Demos Model](#paper-2015-demos-model) - Loads and Runs chemical signalling or compartmental neuronal model from a file.
-- [Recently Loaded Models](#recently-loaded-models) - List of models loaded in MOOSE. (Atleast one model should be loaded)
-- [Connect BioModels](#file-connect-biomodels) - Load chemical signaling models from the BioModels database.
-- [Save](#file-quit) - Saves chemical model to Genesis/SBML format.
-- [Quit](#file-quit) - Quit the interface.
-
-#### View
-
-View menu option provides the following sub options -
-
-- [Editor View](#editor-view) - Switch to the editor view for editing models.
-- [Run View](#run-view) - Switch to run view for running models.
-- [Dock Widgets](#dock-widgets) - Following dock widgets are provided -
- - [Python](#dock-widget-python) - Brings up a full fledged python interpreter integrated with MOOSE GUI. You can interact with loaded models and load new models through the PyMoose API. The entire power of python language is accessible, as well as MOOSE-specific functions and classes.
- - [Edit](#dock-widget-edit) - A property editor for viewing and editing the fields of a selected object such as a pool, enzyme, function or compartment. Editable field values can be changed by clicking on them and overwriting the new values. Please be sure to press enter once the editing is complete, in order to save your changes.
-- [SubWindows](#subwindows) - This allows you to tile or tabify the run and editor views.
-
-#### Help
-
-- [About Moose](#about-moose) - Version and general information about MOOSE.
-- [Built-in documentation](#butilt-in-documentation) - Documentation of MOOSE GUI.
-- [Report a bug](#report-a-bug) - Directs to the github bug tracker for reporting bugs.
-
-### Editor View
-
-The editor view provides two windows -
-
-- [Model Editor](#model-editor) - The model editor is a workspace to edit and create models. Using click-and-drag from the icons in the menu bar, you can create model entities such as chemical pools, reactions, and so on. A click on any object brings its property editor on screen (see below). In objects that can be interconnected, a click also brings up a special arrow icon that is used to connect objects together with messages. You can move objects around within the edit window using click-and-drag. Finally, you can delete objects by selecting one or more, and then choosing the delete option from the pop-up menu.
-The links below is the screenshots point to the details for the chemical signalling model editor.
-
-
-
-- [Property Editor](#property-editor) - The property editor provides a way of viewing and editing the properties of objects selected in the model editor.
-
-
-
-
-### Run View
-
-The Run view, as the name suggests, puts the GUI into a mode where the model can be simulated. As a first step in this, you can click-and-drag an object to the graph window in order to create a time-series plot for that object. For example, in a chemical reaction, you could drag a pool into the graph window and subsequent simulations will display a graph of the concentration of the pool as a function of time.
-Within the Run View window, the time-evolution of the simulation is
-displayed as an animation. For chemical kinetic models, the size of the icons for reactant pools scale to indicate concentration.
-Above the Run View window, there is a special tool bar with a set of simulation controls to run the simulation.
-
-#### Simulation Controls
-
-
-
-This panel allows you to control the various aspects of the simulation.
-
-- [Run Time](#run-time) - Determines duration for which simulation is to run. A simulation which has already run, runs further for the specified additional period.
-- [Reset](#reset) - Restores simulation to its initial state; re-initializes all variables to t = 0.
-- [Stop](#stop) - This button halts an ongoing simulation.
-- [Current time](#current-time) - This reports the current simulation time.
-- [Preferences](#preferences) - Allows you to set simulation and visualization related preferences.
-
-
-#### Plot Widget
-
-
-##### Toolbar
-
-On top of plot window there is a little row of icons:
-
-
-
-These are the plot controls. If you hover the mouse over them for a few seconds, a tooltip pops up. The icons represent the following functions:
-
-*  - Add a new plot window
-
-*  - Deletes current plot window
-
-*  - Toggle X-Y axis grid
-
-*  - Returns the plot display to its default position
-
-*  - Undoes or re-does manipulations you have done to the display.
-
-*  - The plots will pan around with the mouse when you hold the left button down. The plots will zoom with the mouse when you hold the right button down.
-
-*  - With the **`left mouse button`**, this will zoom in to the specified rectangle so that the plots become bigger. With the **`right mouse button`**, the entire plot display will be shrunk to fit into the specified rectangle.
-
-*  - You don't want to mess with these .
-
-*  - Save the plot.
-
-##### Context Menu
-
-The context menu is enabled by right clicking on the plot window. It has the following options -
-
-* **Export to CSV** - Exports the plotted data to CSV format
-* **Toggle Legend** - Toggles the plot legend
-* **Remove** - Provides a list of plotted entities. The selected entity will not be plotted.
diff --git a/moose-core/Docs/user/markdown/Nkit2Documentation.markdown b/moose-core/Docs/user/markdown/Nkit2Documentation.markdown
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-# Introduction
-
-Neuronal models in NeuroML 1.8 format can be loaded and simulated in
-the **MOOSE Graphical User Interface**. The GUI displays the
-neurons in 3D, and allows visual selection and editing of neuronal
-properties. Plotting and visualization of activity proceeds
-concurrently with the simulation. Support for creating and editing
-channels, morphology and networks is planned for the future.
-
-# Neuronal models
-
-Neurons are modeled as equivalent electrical circuits. The
-morphology of a neuron can be broken into isopotential compartments
-connected by axial resistances `R`~`a`~ denoting the cytoplasmic
-resistance. In each compartment, the neuronal membrane is
-represented as a capacitance `C`~`m`~ with a shunt leak resistance `R`~`m`~.
-Electrochemical gradient (due to ion pumps) across the leaky
-membrane causes a voltage drive `E`~`m`~, that hyperpolarizes the inside
-of the cell membrane compared to the outside.
-
-Each voltage dependent ion channel, present on the membrane, is
-modeled as a voltage dependent conductance `G`~`k`~ with gating
-kinetics, in series with an electrochemical voltage drive (battery)
-`E`~`k`~, across the membrane capacitance `C`~`m`~, as in the figure below.
-
-----
-
-
-
-----
-
-Neurons fire action potentials / spikes (sharp rise and fall of
-membrane potential `V`~`m`~) due to voltage dependent channels. These
-result in opening of excitatory / inhibitory synaptic channels
-(conductances with batteries, similar to voltage gated channels) on
-other connected neurons in the network.
-
-MOOSE can handle large networks of detailed neurons, each with
-complicated channel dynamics. Further, MOOSE can integrate chemical
-signaling with electrical activity. Presently, creating and
-simulating these requires PyMOOSE scripting, but these will be
-incorporated into the GUI in the future.
-
-To understand channel kinetics and neuronal action potentials, run
-the Squid Axon demo installed along with MOOSEGUI and consult its
-help/tutorial.
-
-Read more about compartmental modeling in the first few chapters
-of the
-[Book of Genesis](http://www.genesis-sim.org/GENESIS/iBoG/iBoGpdf/index.html).
-
-Models can be defined in [NeuroML](http://www.neuroml.org), an XML
-format which is well supported across simulators. Channels,
-neuronal morphology (compartments), and networks can be specified
-using various levels of NeuroML, namely ChannelML, MorphML and
-NetworkML. Importing of cell models in the
-[GENESIS](http://www.genesis-sim.org/GENESIS) `.p` format is
-supported for backwards compatibitility.
-
-# Neuronal simulations in MOOSEGUI
-
-## Quick start
-
-- MOOSEGUI provides a few neuronal models in moose/Demos directory in
- user's home folder. For example, *File->Load*
- `~/moose/Demos/neuroml/PurkinjeCellPassive/PurkinjePassive.net.xml`, which is a model of the purkinje cell. A 3D rendering of the neuron appears in **`Editor`** tab.
-- Click and drag to rotate, scroll wheel to zoom, and arrow
- keys to pan the 3D rendering.
-- Click to select a compartment on the 3D model. The selected compartment is colored green.
-- An editor will appear on the right hand side where the properties of the compartment can be edited.
-- The 3D view of the model provided by the editor allows only editing of the compartment parameters.
-- In the **`Run`** tab you can see two subwindows. The one on the left provides a dynamic visualization of the compartment Vm as the simulation progresses. The one on the right is the plot window where you can plot the Vm of the various compartments.
-- Press `Ctrl` and click and drag a compartment from the visualizer to the plot window.
-- Run the model using **`Run`** button. You can see the colors of the compartments changing as the simulation progresses. The graphs gets updated simultaneously with the visualizer.
-
-### Editor View
-
-
-
-### Run View
-
-
-## Modeling details
-
-MOOSE uses SI units throughout.
-
-Some salient properties of neuronal building blocks in MOOSE are
-described below. Variables that are updated at every simulation
-time step are are listed **dynamical**. Rest are parameters.
-
-- **Compartment**
- When you select a compartment, you can view and edit its
- properties in the right pane. `V`~`m`~ and `I`~`m`~ are plot-able.
-
- - **`V`~`m`~** : **dynamical** membrane potential (across `C`~`m`~) in Volts.
- - **`C`~`m`~** : membrane capacitance in Farads.
- - **`E`~`m`~** : membrane leak potential in Volts due to the electrochemical
- gradient setup by ion pumps.
- - **`I`~`m`~** : **dynamical** current in Amperes across the membrane via leak
- resistance `R`~`m`~.
- - **`inject`** : current in Amperes injected externally into the compartment.
- - **`initVm`** : initial `V`~`m`~ in Volts.
- - **`R`~`m`~** : membrane leak resistance in Ohms due to leaky channels.
- - **`diameter`** : diameter of the compartment in metres.
- - **`length`** : length of the compartment in metres.
-
- After selecting a compartment, you can click **`See children`** on
- the right pane to list its membrane channels, Ca pool, etc.
-
-- **HHChannel**
- Hodgkin-Huxley channel with voltage dependent dynamical gates.
-
- - **`Gbar`** : peak channel conductance in Siemens.
- - **`E`~`k`~** : reversal potential of the channel, due to electrochemical
- gradient of the ion(s) it allows.
- - **`G`~`k`~** : **dynamical** conductance of the channel in Siemens.
-
- > G~k~(t) = Gbar × X(t)^Xpower^ × Y(t)^Ypower^ × Z(t)^Zpower^
-
- - **`I`~`k`~** : **dynamical** current through the channel into the neuron in
- Amperes.
-
- > I~k~(t) = G~k~(t) × (E~k~-V~m~(t))
-
- - **`X`**, **`Y`**, **`Z`** : **dynamical** gating variables (range `0.0`
- to `1.0`) that may turn on or off as voltage increases with different time
- constants.
-
- > dX(t)/dt = X~inf~/Ï„ - X(t)/Ï„
-
- Here, `X`~`inf`~ and `Ï„` are typically
- sigmoidal/linear/linear-sigmoidal functions of membrane potential
- `V`~`m`~, which are described in a ChannelML file and presently not
- editable from MOOSEGUI. Thus, a gate may open `(X`~`inf`~`(V`~`m`~`) → 1)` or
- close `(X`~`inf`~`(V`~`m`~`) → 0)` on increasing `V`~`m`~, with time constant
- `Ï„(V`~`m`~`)`.
- - **`Xpower`**, **`Ypower`**, **`Zpower`** : powers to which gates are raised in the
- `G`~`k`~`(t)` formula above.
-
-- **HHChannel2D**
- The Hodgkin-Huxley channel2D can have the usual voltage
- dependent dynamical gates, and also gates that dependent on voltage
- and an ionic concentration, as for say Ca-dependent K conductance.
- It has the properties of HHChannel above, and a few more like
- `Xindex` as in the
- [GENESIS tab2Dchannel reference](http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-26.html#ss26.61).
-
-- **CaConc**
- This is a pool of Ca ions in each compartment, in a shell
- volume under the cell membrane. The dynamical Ca concentration
- increases when Ca channels open, and decays back to resting with a
- specified time constant Ï„. Its concentration controls Ca-dependent
- K channels, etc.
- - `Ca` : **dynamical** Ca concentration in the pool in units `mM` ( i.e.,
- `mol/m`^`3`^).
-
- > d[Ca^2+^]/dt = B × I~Ca~ - [Ca^2+^]/τ
-
- - `CaBasal`/`Ca_base` : Base Ca concentration to which the Ca decays
- - `tau` : time constant with which the Ca concentration decays to the
- base Ca level.
- - `B` : constant in the `[Ca`^`2+`^`]` equation above.
- - `thick` : thickness of the Ca shell within the cell membrane which is
- used to calculate `B` (see Chapter 19 of
- [Book of GENESIS](http://www.genesis-sim.org/GENESIS/iBoG/iBoGpdf/index.html).)
-
-
-## Demos
-
-- **Cerebellar granule cell**
- **`File -> Load -> `**
- `~/moose/Demos/neuroml/GranuleCell/GranuleCell.net.xml`
- This is a single compartment Cerebellar granule cell with a variety of
- channels
- [Maex, R. and De Schutter, E., 1997](http://www.tnb.ua.ac.be/models/network.shtml)
- (exported from <http://www.neuroconstruct.org/>). Click on
- its soma, and **See children** for its list of channels. Vary the
- `Gbar` of these channels to obtain regular firing, adapting and
- bursty behaviour (may need to increase tau of the Ca pool).
-
-- **Purkinje cell**
- **`File -> Load -> `**
- `~/moose/Demos/neuroml/PurkinjeCell/Purkinje.net.xml`
- This is a purely passive cell, but with extensive morphology
- [De Schutter, E. and Bower, J. M., 1994] (exported from
- <http://www.neuroconstruct.org/>). The channel
- specifications are in an obsolete ChannelML format which MOOSE does
- not support.
-
-- **Olfactory bulb subnetwork**
- **`File -> Load -> `**
- `~/moose/Demos/neuroml/OlfactoryBulb/numgloms2_seed100.0_decimated.xml`
- This is a pruned and decimated version of a detailed network
- model of the Olfactory bulb [Gilra A. and Bhalla U., in
- preparation] without channels and synaptic connections. We hope to
- post the ChannelML specifications of the channels and synapses
- soon.
-
-- **All channels cell**
- **`File -> Load -> `**
- `~/moose/Demos/neuroml/allChannelsCell/allChannelsCell.net.xml`
- This is the Cerebellar granule cell as above, but with loads of
- channels from various cell types (exported from
- <http://www.neuroconstruct.org/>). Play around with the
- channel properties to see what they do. You can also edit the
- ChannelML files in
- `~/moose/Demos/neuroml/allChannelsCell/cells_channels/` to
- experiment further.
-
-- **NeuroML python scripts**
- In directory `~/moose/Demos/neuroml/GranuleCell`, you can run
- `python FvsI_Granule98.py` which plots firing rate vs injected
- current for the granule cell. Consult this python script to see how
- to read in a NeuroML model and to set up simulations. There are
- ample snippets in `~/moose/Demos/snippets` too.
diff --git a/moose-core/Docs/user/markdown/RdesigneurDocumentation.markdown b/moose-core/Docs/user/markdown/RdesigneurDocumentation.markdown
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------
-
-# **Rdesigneur: Building multiscale models**
-
-Upi Bhalla
-
-Dec 28 2015.
-
------
-
-## Contents
-
-
-## Introduction
-
-**Rdesigneur** (Reaction Diffusion and Electrical SIGnaling in NEURons) is an
-interface to the multiscale modeling capabilities in MOOSE. It is designed
-to build models incorporating biochemical signaling pathways in
-dendrites and spines, coupled to electrical events in neurons. Rdesigneur
-assembles models from predefined parts: it delegates the details to
-specialized model definition formats. Rdesigneur combines one or more of
-the following cell parts to build models:
-
-* Neuronal morphology
-* Dendritic spines
-* Ion channels
-* Reaction systems
-
-Rdesigneur's main role is to specify how these are put together, including
-assigning parameters to do so. Rdesigneur also helps with setting up the
-simulation input and output.
-
-## Quick Start
-Here we provide a few use cases, building up from a minimal model to a
-reasonably complete multiscale model spanning chemical and electrical signaling.
-
-### Bare Rdesigneur: single passive compartment
-If we don't provide any arguments at all to the Rdesigneur, it makes a model
-with a single passive electrical compartment in the MOOSE path
-`/model/elec/soma`. Here is how to do this:
-
- import moose
- import rdesigneur as rd
- rdes = rd.rdesigneur()
- rdes.buildModel()
-
-To confirm that it has made a compartment with some default values we can add
-a line:
-
- moose.showfields( rdes.soma )
-
-This should produce the output:
-
- [ /model[0]/elec[0]/soma[0] ]
- diameter = 0.0005
- fieldIndex = 0
- Ra = 7639437.26841
- y0 = 0.0
- Rm = 424413.177334
- index = 0
- numData = 1
- inject = 0.0
- initVm = -0.065
- Em = -0.0544
- y = 0.0
- numField = 1
- path = /model[0]/elec[0]/soma[0]
- dt = 0.0
- tick = -2
- z0 = 0.0
- name = soma
- Cm = 7.85398163398e-09
- x0 = 0.0
- Vm = -0.06
- className = ZombieCompartment
- idValue = 465
- length = 0.0005
- Im = 1.3194689277e-08
- x = 0.0005
- z = 0.0
-
-
-### Simulate and display current pulse to soma
-A more useful script would run and display the model. Rdesigneur can help with
-the stimulus and the plotting. This simulation has the same passive
-compartment, and current is injected as the simulation runs.
-This script displays the membrane potential of the soma as it charges and
-discharges.
-
- import moose
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- stimList = [['soma', '1', '.', 'inject', '(t>0.1 && t<0.2) * 2e-8']],
- plotList = [['soma', '1', '.', 'Vm', 'Soma membrane potential']],
- )
- rdes.buildModel()
- moose.reinit()
- moose.start( 0.3 )
- rdes.display()
-
-The *stimList* defines a stimulus. Each entry has five arguments:
-
- `[region_in_cell, region_expression, moose_object, parameter, expression_string]`
-
-+ `region_in_cell` specifies the objects to stimulate. Here it is just the
- soma.
-+ `region_expression` specifies a geometry based calculation to decide
- whether to apply the stimulus. The value must be >0 for the stimulus
- to be present. Here it is just 1.
- `moose_object` specifies the simulation object to operate upon during
- the stimulus. Here the `.` means that it is the soma itself. In other
- models it might be a channel on the soma, or a synapse, and so on.
-+ `parameter` specifies the simulation parameter on the moose object that
- the stimulus will modify. Here it is
- the injection current to the soma compartment.
-+ `expression_string` calculates the value of the parameter, typically
- as a function of time. Here we use the function
- `(t>0.1 && t<0.2) * 2e-8` which evaluates as 2e-8 between the times of
- 0.1 and 0.2 seconds.
-
-To summarise this, the *stimList* here means *inject a current of 20nA to the
-soma between the times of 0.1 and 0.2 s*.
-
-The *plotList* defines what to plot. It has a similar set of arguments:
-
- `[region_in_cell, region_expression, moose_object, parameter, title_of_plot]`
-These mean the same thing as for the stimList except for the title of the plot.
-
-The *rdes.display()* function causes the plots to be displayed.
-
-
-
-When we run this we see an initial depolarization as the soma settles from its
-initial -65 mV to a resting Em = -54.4 mV. These are the original HH values, see
-the example above. At t = 0.1 seconds there is another depolarization due
-to the current injection, and at t = 0.2 seconds this goes back to the resting
-potential.
-
-### HH Squid model in a single compartment
-Here we put the Hodgkin-Huxley squid model channels into a passive compartment.
-The HH channels are predefined as prototype channels for Rdesigneur,
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- chanProto = [['make_HH_Na()', 'Na'], ['make_HH_K()', 'K']],
- chanDistrib = [
- ['Na', 'soma', 'Gbar', '1200' ],
- ['K', 'soma', 'Gbar', '360' ]],
- stimList = [['soma', '1', '.', 'inject', '(t>0.1 && t<0.2) * 1e-8' ]],
- plotList = [['soma', '1', '.', 'Vm', 'Membrane potential']]
- )
-
- rdes.buildModel()
- moose.reinit()
- moose.start( 0.3 )
- rdes.display()
-
-
-Here we introduce two new model specification lines:
-
-+ **chanProto**: This specifies which ion channels will be used in the
- model.
- Each entry here has two fields: the source of the channel definition,
- and (optionally) the name of the channel.
- In this example we specify two channels, an Na and a K channel using
- the original Hodgkin-Huxley parameters. As the source of the channel
- definition we use the name of the Python function that builds the
- channel. The *make_HH_Na()* and *make_HH_K()* functions are predefined
- but we can also specify our own functions for making prototypes.
- We could also have specified the channel prototype using the name
- of a channel definition file in ChannelML (a subset of NeuroML) format.
-+ **chanDistrib**: This specifies *where* the channels should be placed
- over the geometry of the cell. Each entry in the chanDistrib list
- specifies the distribution of parameters for one channel using four
- entries:
-
- `[object_name, region_in_cell, parameter, expression_string]`
-
- In this case the job is almost trivial, since we just have a single
- compartment named *soma*. So the line
-
- `['Na', 'soma', 'Gbar', '1200' ]`
-
- means *Put the Na channel in the soma, and set its maximal
- conductance density (Gbar) to 1200 Siemens/m^2*.
-
-As before we apply a somatic current pulse. Since we now have HH channels in
-the model, this generates action potentials.
-
-
-
-
-### Reaction system in a single compartment
-Here we use the compartment as a place in which to embed a chemical model.
-The chemical oscillator model is predefined in the rdesigneur prototypes.
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- turnOffElec = True,
- diffusionLength = 1e-3, # Default diffusion length is 2 microns
- chemProto = [['makeChemOscillator()', 'osc']],
- chemDistrib = [['osc', 'soma', 'install', '1' ]],
- plotList = [['soma', '1', 'dend/a', 'conc', 'a Conc'],
- ['soma', '1', 'dend/b', 'conc', 'b Conc']]
- )
- rdes.buildModel()
- b = moose.element( '/model/chem/dend/b' )
- b.concInit *= 5
- moose.reinit()
- moose.start( 200 )
-
- rdes.display()
-
-In this special case we set the turnOffElec flag to True, so that Rdesigneur
-only sets up chemical and not electrical calculations. This makes the
-calculations much faster, since we disable electrical calculations and delink
-chemical calculations from them.
-
-We also have a line which sets the `diffusionLength` to 1 mm, so that it is
-bigger than the 0.5 mm squid axon segment in the default compartment. If you
-don't do this the system will subdivide the compartment into the default
-2 micron voxels for the purposes of putting in a reaction-diffusion system.
-We discuss this case below.
-
-Note how the *plotList* is done here. To remind you, each entry has five
-arguments
-
- [region_in_cell, region_expression, moose_object, parameter, title_of_plot]
-
-The change from the earlier usage is that the `moose_object` now refers to
-a chemical entity, in this example the molecule *dend/a*. The simulator
-builds a default chemical compartment named *dend* to hold the reactions
-defined in the *chemProto*. What we do in this plot is to select molecule *a*
-sitting in *dend*, and plot its concentration. Then we do this again for
-molecule *b*.
-
-After the model is built, we add a couple of lines to change the
-initial concentration of the molecular pool *b*. Note its full path within
-MOOSE: */model/chem/dend/b*. It is scaled up 5x to give rise to slowly
-decaying oscillations.
-
-
-
-### Reaction-diffusion system
-
-In order to see what a reaction-diffusion system looks like, delete the
-`diffusionLength` expression in the previous example and add a couple of lines
-to set up 3-D graphics for the reaction-diffusion product:
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- turnOffElec = True,
- chemProto = [['makeChemOscillator()', 'osc']],
- chemDistrib = [['osc', 'soma', 'install', '1' ]],
- plotList = [['soma', '1', 'dend/a', 'conc', 'Concentration of a'],
- ['soma', '1', 'dend/b', 'conc', 'Concentration of b']],
- moogList = [['soma', '1', 'dend/a', 'conc', 'a Conc', 0, 360 ]]
- )
-
- rdes.buildModel()
- bv = moose.vec( '/model/chem/dend/b' )
- bv[0].concInit *= 2
- bv[-1].concInit *= 2
- moose.reinit()
-
- rdes.displayMoogli( 1, 400, 0.001 )
-
-
-
-This is the line we deleted.
-
- diffusionLength = 1e-3,
-
-With this change we permit
-*rdesigneur* to use the default diffusion length of 2 microns.
-The 500-micron axon segment is now subdivided into 250 voxels, each of
-which has a reaction system and diffusing molecules. To make it more
-picturesque, we have added a line after the plotList, to display the outcome
-in 3-D:
-
- moogList = [['soma', '1', 'dend/a', 'conc', 'a Conc', 0, 360 ]]
-
-This line says: take the model compartments defined by `soma` as the region
-to display, do so throughout the the geometry (the `1` signifies this), and
-over this range find the chemical entity defined by `dend/a`. For each `a`
-molecule, find the `conc` and dsiplay it. There are two optional arguments,
-`0` and `360`, which specify the low and high value of the displayed variable.
-
-In order to initially break the symmetry of the system, we change the initial
-concentration of molecule b at each end of the cylinder:
-
- bv[0].concInit *= 2
- bv[-1].concInit *= 2
-
-If we didn't do this the entire system would go through a few cycles of
-decaying oscillation and then reach a boring, spatially uniform, steady state.
-Try putting an initial symmetry break elsewhere to see what happens.
-
-To display the concenctration changes in the 3-D soma as the simulation runs,
-we use the line
-
- `rdes.displayMoogli( 1, 400, 0.001 )`
-
-The arguments mean: *displayMoogli( frametime, runtime, rotation )*
-Here,
-
- frametime = time by which simulation advances between display updates
- runtime = Total simulated time
- rotation = angle by which display rotates in each frame, in radians.
-
-When we run this, we first get a 3-D display with the oscillating
-reaction-diffusion system making its way inward from the two ends. After the
-simulation ends the plots for all compartments for the whole run come up.
-
-
-
-
-### Primer on using the 3-D MOOGLI display
-Here is a short primer on the 3-D display controls.
-
-- *Roll, pitch, and yaw*: Use the letters *r*, *p*, and *y*. To rotate
-backwards, use capitals.
-- *Zoom out and in*: Use the *,* and *.* keys, or their upper-case equivalents,
-*<* and *>*. Easier to remember if you think in terms of the upper-case.
-- *Left/right/up/down*: Arrow keys.
-- *Quit*: control-q or control-w.
-- You can also use the mouse or trackpad to control most of the above.
-- By default rdesigneur gives Moogli a small rotation each frame. It is the
-*rotation* argument in the line:
-
- `displayMoogli( frametime, runtime, rotation )`
-
-These controls operate over and above this rotation, but the rotation
-continues. If you set the rotation to zero you can, with a suitable flick of
-the mouse, get the image to rotate in any direction you choose as long as the
-window is updating.
-
-### Make a toy multiscale model with electrical and chemical signaling.
-Now we put together chemical and electrical models. In this toy model we have an
-HH-squid type single compartment electrical model, cohabiting with a chemical
-oscillator. The chemical oscillator regulates K+ channel amounts, and the
-average membrane potential regulates the amounts of a reactant in the
-chemical oscillator. This is a recipe for some strange firing patterns.
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- # We want just one compartment so we set diffusion length to be
- # bigger than the 0.5 mm HH axon compartment default.
- diffusionLength = 1e-3,
- chanProto = [['make_HH_Na()', 'Na'], ['make_HH_K()', 'K']],
- chanDistrib = [
- ['Na', 'soma', 'Gbar', '1200' ],
- ['K', 'soma', 'Gbar', '360' ]],
- chemProto = [['makeChemOscillator()', 'osc']],
- chemDistrib = [['osc', 'soma', 'install', '1' ]],
- # These adaptor parameters give interesting-looking but
- # not particularly physiological behaviour.
- adaptorList = [
- [ 'dend/a', 'conc', 'Na', 'modulation', 1, -5.0 ],
- [ 'dend/b', 'conc', 'K', 'modulation', 1, -0.2],
- [ 'dend/b', 'conc', '.', 'inject', -1.0e-7, 4e-7 ],
- [ '.', 'Vm', 'dend/s', 'conc', 2.5, 20.0 ]
- ],
- plotList = [['soma', '1', 'dend/a', 'conc', 'a Conc'],
- ['soma', '1', 'dend/b', 'conc', 'b Conc'],
- ['soma', '1', 'dend/s', 'conc', 's Conc'],
- ['soma', '1', 'Na', 'Gk', 'Na Gk'],
- ['soma', '1', '.', 'Vm', 'Membrane potential']
- ]
- )
-
- rdes.buildModel()
- moose.reinit()
- moose.start( 250 ) # Takes a few seconds to run this.
-
- rdes.display()
-
-We've already modeled the HH squid model and the oscillator individually,
-and you should recognize the parts of those models above.
-The new section that makes this work the *adaptorList* which specifies how
-the electrical and chemical parts talk to each other. This entirely
-fictional set of interactions goes like this:
-
- [ 'dend/a', 'conc', 'Na', 'modulation', 1, -5.0 ]
-
-+ *dend/a*: The originating variable comes from the 'a' pool on the
- 'dend' compartment.
-
- *conc*: This is the originating variable name on the 'a' pool.
-
- *Na*: This is the target variable
-
- *modulation*: scale the Gbar of Na up and down. Use 'modulation'
- rather than direct assignment of Gbar since Gbar is different for
- each differently-sized compartment.
-
- *1*: This is the initial offset
-
- *-5.0*: This is the scaling from the input to the parameter updated
- in the simulation.
-
-A similar set of adaptor entries couple the molecule *dend/b* to the
-K channel, *dend/b* again to the current injection into the soma, and the
-membrane potential to the concentration of *dend/s*.
-
-
-
-
-### Morphology: Load .swc morphology file and view it
-Here we build a passive model using a morphology file in the .swc file format
-(as used by NeuroMorpho.org). The morphology file is predefined for Rdesigneur
-and resides in the
-directory `./cells`. We apply a somatic current pulse, and view
-the somatic membrane potential in a plot, as before.
-To make things interesting we display the morphology in 3-D upon which we
-represent the membrane potential as colors.
-
- import moose
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- cellProto = [['./cells/h10.CNG.swc', 'elec']],
- stimList = [['soma', '1', '.', 'inject', 't * 25e-9' ]],
- plotList = [['#', '1', '.', 'Vm', 'Membrane potential'],
- ['#', '1', 'Ca_conc', 'Ca', 'Ca conc (uM)']],
- moogList = [['#', '1', '.', 'Vm', 'Soma potential']]
- )
-
- rdes.buildModel()
-
- moose.reinit()
- rdes.displayMoogli( 0.0002, 0.1 )
-
-Here the new concept is the cellProto line, which loads in the specified cell
-model:
-
- `[ filename, cellname ]`
-
-The system recognizes the filename extension and builds a model from the swc
-file. It uses the cellname **elec** in this example.
-
-We use a similar line as in the reaction-diffusion example, to build up a
-Moogli display of the cell model:
-
- `moogList = [['#', '1', '.', 'Vm', 'Soma potential']]`
-
-Here we have:
-
- *#*: the path to use for selecting the compartments to display.
- This wildcard means use all compartments.
- *1*: The expression to use for the compartments. Again, `1` means use
- all of them.
- *.*: Which object in the compartment to display. Here we are using the
- compartment itself, so it is just a dot.
- *Vm*: Field to display
- *Soma potential*: Title for display.
-
-
-
-### Build an active neuron model by putting channels into a morphology file
-We load in a morphology file and distribute voltage-gated ion channels over
-the neuron. Here the voltage-gated channels are obtained from a number of
-channelML files, located in the `./channels` subdirectory. Since we have a
-spatially extended neuron, we need to specify the spatial distribution of
-channel densities too.
-
-
- import moose
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- chanProto = [
- ['./chans/hd.xml'],
- ['./chans/kap.xml'],
- ['./chans/kad.xml'],
- ['./chans/kdr.xml'],
- ['./chans/na3.xml'],
- ['./chans/nax.xml'],
- ['./chans/CaConc.xml'],
- ['./chans/Ca.xml']
- ],
- cellProto = [['./cells/h10.CNG.swc', 'elec']],
- chanDistrib = [ \
- ["hd", "#dend#,#apical#", "Gbar", "50e-2*(1+(p*3e4))" ],
- ["kdr", "#", "Gbar", "p < 50e-6 ? 500 : 100" ],
- ["na3", "#soma#,#dend#,#apical#", "Gbar", "850" ],
- ["nax", "#soma#,#axon#", "Gbar", "1250" ],
- ["kap", "#axon#,#soma#", "Gbar", "300" ],
- ["kap", "#dend#,#apical#", "Gbar",
- "300*(H(100-p*1e6)) * (1+(p*1e4))" ],
- ["Ca_conc", "#", "tau", "0.0133" ],
- ["kad", "#soma#,#dend#,#apical#", "Gbar", "50" ],
- ["Ca", "#", "Gbar", "50" ]
- ],
- stimList = [['soma', '1', '.', 'inject', '(t>0.02) * 1e-9' ]],
- plotList = [['#', '1', '.', 'Vm', 'Membrane potential'],
- ['#', '1', 'Ca_conc', 'Ca', 'Ca conc (uM)']],
- moogList = [['#', '1', 'Ca_conc', 'Ca', 'Calcium conc (uM)', 0, 120],
- ['#', '1', '.', 'Vm', 'Soma potential']]
- )
-
- rdes.buildModel()
-
- moose.reinit()
- rdes.displayMoogli( 0.0002, 0.052 )
-
-
-Here we make more extensive use of two concepts which we've already seen from
-the single compartment squid model:
-
-1. *chanProto*: This defines numerous channels, each of which is of the form:
-
- `[ filename ]`
-
- or
-
- `[ filename, channelname ]`
-
-If the *channelname* is not specified the system uses the last part of the
-channel name, before the filetype suffix.
-
-2. *chanDistrib*: This defines the spatial distribution of each channel type.
-Each line is of a form that should be familiar now:
-
- `[channelname, region_in_cell, parameter, expression_string]`
-
-- The *channelname* is the name of the prototype from *chanproto*. This is
-usually an ion channel, but in the example above you can also see a calcium
-concentration pool defined.
-- The *region_in_cell* is typically defined using wildcards, so that it
-generalizes to any cell morphology.
-For example, the plain wildcard `#` means to consider
-all cell compartments. The wildcard `#dend#` means to consider all compartments with the string `dend`
-somewhere in the name. Wildcards can be comma-separated, so
-`#soma#,#dend#` means consider all compartments with either soma or dend in
-their name. The naming in MOOSE is defined by the model file. Importantly,
-in **.swc** files MOOSE generates names that respect the classification of
-compartments into axon, soma, dendrite, and apical dendrite compartments
-respectively. SWC files generate compartment names such as:
-
- soma_<number>
- dend_<number>
- apical_<number>
- axon_<number>
-
-where the number is automatically assigned by the reader. In order to
-select all dendritic compartments, for example, one would use *"#dend#"*
-where the *"#"* acts as a wildcard to accept any string.
-- The *parameter* is usually Gbar, the channel conductance density in *S/m^2*.
-If *Gbar* is zero or less, then the system economizes by not incorporating this
-channel mechanism in this part of the cell. Similarly, for calcium pools, if
-the *tau* is below zero then the calcium pool object is simply not inserted
-into this part of the cell.
-- The *expression_string* defines the value of the parameter, such as Gbar.
-This is typically a function of position in the cell. The expression evaluator
-knows about several parameters of cell geometry. All units are in metres:
-
-+ *x*, *y* and *z* coordinates.
-+ *g*, the geometrical distance from the soma
-+ *p*, the path length from the soma, measured along the dendrites.
-+ *dia*, the diameter of the dendrite.
-+ *L*, The electrotonic length from the soma (no units).
-
-Along with these geometrical arguments, we make liberal use of the Heaviside
-function H(x) to set up the channel distributions. The expression evaluator
-also knows about pretty much all common algebraic, trignometric, and logarithmic
-functions, should you wish to use these.
-
-Also note the two Moogli displays. The first is the calcium
-concentration. The second is the membrane potential in each compartment. Easy!
-
-
-
-### Build a spiny neuron from a morphology file and put active channels in it.
-This model is one step elaborated from the previous one, in that we now also
-have dendritic spines. MOOSE lets one decorate a bare neuronal morphology file
-with dendritic spines, specifying various geometric parameters of their
-location. As before, we use an swc file for the morphology, and the same
-ion channels and distribution.
-
- import moose
- import pylab
- import rdesigneur as rd
- rdes = rd.rdesigneur(
- chanProto = [
- ['./chans/hd.xml'],
- ['./chans/kap.xml'],
- ['./chans/kad.xml'],
- ['./chans/kdr.xml'],
- ['./chans/na3.xml'],
- ['./chans/nax.xml'],
- ['./chans/CaConc.xml'],
- ['./chans/Ca.xml']
- ],
- cellProto = [['./cells/h10.CNG.swc', 'elec']],
- spineProto = [['makeActiveSpine()', 'spine']],
- chanDistrib = [
- ["hd", "#dend#,#apical#", "Gbar", "50e-2*(1+(p*3e4))" ],
- ["kdr", "#", "Gbar", "p < 50e-6 ? 500 : 100" ],
- ["na3", "#soma#,#dend#,#apical#", "Gbar", "850" ],
- ["nax", "#soma#,#axon#", "Gbar", "1250" ],
- ["kap", "#axon#,#soma#", "Gbar", "300" ],
- ["kap", "#dend#,#apical#", "Gbar",
- "300*(H(100-p*1e6)) * (1+(p*1e4))" ],
- ["Ca_conc", "#", "tau", "0.0133" ],
- ["kad", "#soma#,#dend#,#apical#", "Gbar", "50" ],
- ["Ca", "#", "Gbar", "50" ]
- ],
- spineDistrib = [['spine', '#dend#,#apical#', '20e-6', '1e-6']],
- stimList = [['soma', '1', '.', 'inject', '(t>0.02) * 1e-9' ]],
- plotList = [['#', '1', '.', 'Vm', 'Membrane potential'],
- ['#', '1', 'Ca_conc', 'Ca', 'Ca conc (uM)']],
- moogList = [['#', '1', 'Ca_conc', 'Ca', 'Calcium conc (uM)', 0, 120],
- ['#', '1', '.', 'Vm', 'Soma potential']]
- )
-
- rdes.buildModel()
-
- moose.reinit()
- rdes.displayMoogli( 0.0002, 0.023 )
-
-
-Spines are set up in a familiar way: we first define one (or more) prototype
-spines, and then distribute these around the cell. Here is the prototype
-string:
-
- [spine_proto, spinename]
-
-*spineProto*: This is typically a function. One can define one's own,
-but there are several predefined ones in rdesigneur. All these define a
-spine with the following parameters:
-
-- head diameter 0.5 microns
-- head length 0.5 microns
-- shaft length 1 micron
-- shaft diameter of 0.2 microns
-- RM = 1.0 ohm-metre square
-- RA = 1.0 ohm-meter
-- CM = 0.01 Farads per square metre.
-
-Here are the predefined spine prototypes:
-
-- *makePassiveSpine()*: This just makes a passive spine with the
-default parameters
-- *makeExcSpine()*: This makes a spine with NMDA and glu receptors,
-and also a calcium pool. The NMDA channel feeds the Ca pool.
-- *makeActiveSpine()*: This adds a Ca channel to the exc_spine.
-and also a calcium pool.
-
-The spine distributions are specified in a familiar way for the first few
-arguments, and then there are multiple (optional) spine-specific parameters:
-
-*[spinename, region_in_cell, spacing, spacing_distrib, size, size_distrib, angle, angle_distrib ]*
-
-Only the first two arguments are mandatory.
-
-- *spinename*: The prototype name
-- *region_in_cell*: Usual wildcard specification of names of compartments in which to put the spines.
-- *spacing*: Math expression to define spacing between spines. In the current implementation this evaluates to `1/probability_of_spine_per_unit_length`.
-Defaults to 10 microns. Thus, there is a 10% probability of a spine insertion in every micron. This evaluation method has the drawback that it is possible to space spines rather too close to each other. If spacing is zero or less, no spines are inserted.
-- *spacing_distrib*: Math expression for distribution of spacing. In the current implementation, this specifies the interval at which the system samples from the spacing probability above. Defaults to 1 micron.
-- *size*: Linear scale factor for size of spine. All dimensions are scaled by this factor. The default spine head here is 0.5 microns in diameter and length. If the scale factor were to be 2, the volume would be 8 times as large. Defaults to 1.0.
-- *size_distrib*: Range for size of spine. A random number R is computed in the range 0 to 1, and the final size used is `size + (R - 0.5) * size_distrib`. Defaults to 0.5
-- *angle*: This specifies the initial angle at which the spine sticks out of the dendrite. If all angles were zero, they would all point away from the soma. Defaults to 0 radians.
-- *angle_distrib*: Specifies a random number to add to the initial angle. Defaults to 2 PI radians, so the spines come out in any direction.
-
-One may well ask why we are not using a Python dictionary to handle all
-these parameters. Short answer is: terseness. Longer answer is that the
-rdesigneur format is itself meant to be an intermediate form for an
-eventual high-level, possibly XML-based multiscale modeling format.
-
-
-
-### Build a spiny neuron from a morphology file and put a reaction-diffusion system in it.
-Rdesigneur is specially designed to take reaction systems with a dendrite,
-a spine head, and a spine PSD compartment, and embed these systems into
-neuronal morphologies. This example shows how this is done.
-
-The dendritic molecules diffuse along the dendrite
-in the region specified by the *chemDistrib* keyword. In this case they are
-placed on all apical and basal dendrites, but only at distances over
-500 microns from the soma. The spine head and PSD
-reaction systems are inserted only into spines within this same *chemDistrib*
-zone. Diffusion coupling between dendrite, and each spine head and PSD is also
-set up.
-It takes a predefined chemical model file for Rdesigneur, which resides
-in the `./chem` subdirectory. As in an earlier example, we turn off the
-electrical calculations here as they are not needed.
-Here we plot out the number of receptors on every single spine as a function
-of time.
-
-(Documentation still to come here)
-
-### Make a full multiscale model with complex spiny morphology and electrical and chemical signaling.
-
-(Documentation still to come here)
diff --git a/moose-core/Docs/user/markdown/index.markdown b/moose-core/Docs/user/markdown/index.markdown
deleted file mode 100644
index 3ff944ded79687bae169d7f90d2ecb667d67c717..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/markdown/index.markdown
+++ /dev/null
@@ -1,12 +0,0 @@
-% User documentation for MOOSE
-% Niraj Dudani
-% January 1, 2013
-
-Index for all documents
------------------------
-
-- [Getting started with python scripting for MOOSE](html/pymoose2walkthrough.html)
-- [MOOSEGUI: Graphical interface for MOOSE](html/MooseGuiDocs.html)
-- [Neuronal simulations in MOOSEGUI](html/Nkit2Documentation.html)
-- [Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI](html/Kkit12Documentation.html)
-- [Documentation for all MOOSE classes and functions](html/moosebuiltindocs.html)
diff --git a/moose-core/Docs/user/markdown/markdown2rst.py b/moose-core/Docs/user/markdown/markdown2rst.py
deleted file mode 100644
index 7544a450b92173af152ca43dc79692abb69d077b..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/markdown/markdown2rst.py
+++ /dev/null
@@ -1,14 +0,0 @@
-import os
-import subprocess
-
-file_list = ["MooseGuiDocs","Kkit12Documentation","RdesigneurDocumentation"]
-
-DOCUMENTATION_DESTINATION_DIR = '../GUI/'
-SOURCE_EXTENSION = '.markdown'
-OUTPUT_EXTENSION = '.rst'
-for filename in file_list:
- source_file = filename + SOURCE_EXTENSION
- output_file = DOCUMENTATION_DESTINATION_DIR + filename + OUTPUT_EXTENSION
- command = 'pandoc -s {0} -o {1}'.format(source_file, output_file)
- print(command)
- subprocess.call(command.split(' '))
diff --git a/moose-core/Docs/user/markdown/moosebuiltindocs.markdown b/moose-core/Docs/user/markdown/moosebuiltindocs.markdown
deleted file mode 100644
index 50b2eb3639c62c2db07f876c3edc40d18193aa13..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/markdown/moosebuiltindocs.markdown
+++ /dev/null
@@ -1,7862 +0,0 @@
-% Documentation for all MOOSE classes and functions
-% As visible in the Python module
-% Auto-generated on January 07, 2013
-
-# Index for MOOSE Classes
----- ---- ---- ---- ---- ----
-**A** [`Enz`](#enz) [`Interpol2D`](#interpol2d) [`NMDAChan`](#nmdachan) [`Species`](#species) [`VectorTable`](#vectortable)
-[`Adaptor`](#adaptor) [`EnzBase`](#enzbase) [`IntFire`](#intfire) **O** [`SpherePanel`](#spherepanel) **Z**
-[`Annotator`](#annotator) **F** [`IzhikevichNrn`](#izhikevichnrn) [`OneToAllMsg`](#onetoallmsg) [`SpikeGen`](#spikegen) [`ZBufPool`](#zbufpool)
-[`Arith`](#arith) [`Finfo`](#finfo) **L** [`OneToOneMsg`](#onetoonemsg) [`Stats`](#stats) [`ZEnz`](#zenz)
-**B** [`FuncBase`](#funcbase) [`LeakyIaF`](#leakyiaf) **P** [`StimulusTable`](#stimulustable) [`ZFuncPool`](#zfuncpool)
-[`Boundary`](#boundary) [`FuncPool`](#funcpool) **M** [`Panel`](#panel) [`Stoich`](#stoich) [`ZMMenz`](#zmmenz)
-[`BufPool`](#bufpool) **G** [`MarkovChannel`](#markovchannel) [`PIDController`](#pidcontroller) [`StoichCore`](#stoichcore) [`ZombieBufPool`](#zombiebufpool)
-**C** [`Geometry`](#geometry) [`MarkovGslSolver`](#markovgslsolver) [`Pool`](#pool) [`StoichPools`](#stoichpools) [`ZombieCaConc`](#zombiecaconc)
-[`CaConc`](#caconc) [`GHK`](#ghk) [`MarkovRateTable`](#markovratetable) [`PoolBase`](#poolbase) [`SumFunc`](#sumfunc) [`ZombieCompartment`](#zombiecompartment)
-[`ChanBase`](#chanbase) [`Group`](#group) [`MarkovSolver`](#markovsolver) [`Port`](#port) [`Surface`](#surface) [`ZombieEnz`](#zombieenz)
-[`ChemMesh`](#chemmesh) [`GslIntegrator`](#gslintegrator) [`MarkovSolverBase`](#markovsolverbase) [`PulseGen`](#pulsegen) [`SymCompartment`](#symcompartment) [`ZombieFuncPool`](#zombiefuncpool)
-[`Cinfo`](#cinfo) [`GslStoich`](#gslstoich) [`MathFunc`](#mathfunc) **R** [`Synapse`](#synapse) [`ZombieHHChannel`](#zombiehhchannel)
-[`Clock`](#clock) [`GssaStoich`](#gssastoich) [`Mdouble`](#mdouble) [`RC`](#rc) [`SynBase`](#synbase) [`ZombieMMenz`](#zombiemmenz)
-[`Compartment`](#compartment) **H** [`MeshEntry`](#meshentry) [`Reac`](#reac) [`SynChan`](#synchan) [`ZombiePool`](#zombiepool)
-[`CplxEnzBase`](#cplxenzbase) [`HDF5DataWriter`](#hdf5datawriter) [`MgBlock`](#mgblock) [`ReacBase`](#reacbase) [`SynChanBase`](#synchanbase) [`ZombieReac`](#zombiereac)
-[`CubeMesh`](#cubemesh) [`HDF5WriterBase`](#hdf5writerbase) [`MMenz`](#mmenz) [`RectPanel`](#rectpanel) **T** [`ZombieSumFunc`](#zombiesumfunc)
-[`CylMesh`](#cylmesh) [`HemispherePanel`](#hemispherepanel) [`Msg`](#msg) [`ReduceMsg`](#reducemsg) [`Table`](#table) [`ZPool`](#zpool)
-[`CylPanel`](#cylpanel) [`HHChannel`](#hhchannel) [`Mstring`](#mstring) **S** [`TableBase`](#tablebase) [`ZReac`](#zreac)
-**D** [`HHChannel2D`](#hhchannel2d) **N** [`Shell`](#shell) [`TableEntry`](#tableentry)
-[`DiagonalMsg`](#diagonalmsg) [`HHGate`](#hhgate) [`Nernst`](#nernst) [`SimManager`](#simmanager) [`testSched`](#testsched)
-[`DiffAmp`](#diffamp) [`HHGate2D`](#hhgate2d) [`NeuroMesh`](#neuromesh) [`SingleMsg`](#singlemsg) [`Tick`](#tick)
-[`DiskPanel`](#diskpanel) [`HSolve`](#hsolve) [`Neuron`](#neuron) [`SolverJunction`](#solverjunction) [`TriPanel`](#tripanel)
-**E** **I** [`Neutral`](#neutral) [`SparseMsg`](#sparsemsg) **V**
----- ---- ---- ---- ---- ----
-
-
-# Index for MOOSE Functions
----- ---- ---- ---- ---- ----
-**C** [`element`](#element) [`getmoosedoc`](#getmoosedoc) [`move`](#move) [`saveModel`](#savemodel) [`stop`](#stop)
-[`ce`](#ce) [`exists`](#exists) **I** **P** [`seed`](#seed) [`syncDataHandler`](#syncdatahandler)
-[`connect`](#connect) **G** [`isRunning`](#isrunning) [`pwe`](#pwe) [`setClock`](#setclock) **U**
-[`copy`](#copy) [`getCwe`](#getcwe) **L** **Q** [`setCwe`](#setcwe) [`useClock`](#useclock)
-**D** [`getField`](#getfield) [`le`](#le) [`quit`](#quit) [`showfield`](#showfield) **W**
-[`delete`](#delete) [`getFieldDict`](#getfielddict) [`listmsg`](#listmsg) **R** [`showfields`](#showfields) [`wildcardFind`](#wildcardfind)
-[`doc`](#doc) [`getfielddoc`](#getfielddoc) [`loadModel`](#loadmodel) [`reinit`](#reinit) [`showmsg`](#showmsg) [`writeSBML`](#writesbml)
-**E** [`getFieldNames`](#getfieldnames) **M** **S** [`start`](#start)
----- ---- ---- ---- ---- ----
-
-# MOOSE Classes
-
-
-## Adaptor
-**Author**: Upinder S. Bhalla, 2008, NCBS
-
-**Description**: Averages and rescales values to couple different kinds of simulation
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`inputOffset`** `double` Offset to apply to input message, before scaling
-**`outputOffset`** `double` Offset to apply at output, after scaling
-**`scale`** `double` Scaling factor to apply to input
-**`output`** `double` This is the linearly transformed output.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`outputSrc`** `double` Sends the output value every timestep.
-**`requestInput`** `void` Sends out the request. Issued from the process call.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`input`** `double` Input message to the adaptor. If multiple inputs are received, the system averages the inputs.
-**`process`** `void` Handles 'process' call
-**`reinit`** `void` Handles 'reinit' call
-**`handleInput`** `double` Handle the returned value.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` This is a shared message to receive Process message from the scheduler.
-**`inputRequest`** `void` This is a shared message to request and handle value messages from fields.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Annotator
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`x`** `double` x field. Typically display coordinate x
-**`y`** `double` y field. Typically display coordinate y
-**`z`** `double` z field. Typically display coordinate z
-**`notes`** `string` A string to hold some text notes about parent object
-**`color`** `string` A string to hold a text string specifying display color.Can be a regular English color name, or an rgb code rrrgggbbb
-**`textColor`** `string` A string to hold a text string specifying color for text labelthat might be on the display for this object.Can be a regular English color name, or an rgb code rrrgggbbb
-**`icon`** `string` A string to specify icon to use for display
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Arith
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`function`** `string` Arithmetic function to perform on inputs.
-**`outputValue`** `double` Value of output as computed last timestep.
-**`arg1Value`** `double` Value of arg1 as computed last timestep.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`output`** `double` Sends out the computed value
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`arg1`** `double` Handles argument 1. This just assigns it
-**`arg2`** `double` Handles argument 2. This just assigns it
-**`arg3`** `double` Handles argument 3. This sums in each input, and clears each clock tick.
-**`arg1x2`** `double,double` Store the product of the two arguments in output_
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`anyValue`** `unsigned int,double` Value of any of the internal fields, output, arg1, arg2, arg3,as specified by the index argument from 0 to 3.
-
-
-## Boundary
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`reflectivity`** `double` What happens to a molecule hitting it: bounces, absorbed, diffused?
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toAdjacent`** `void` Dummy message going to adjacent compartment.
-**`toInside`** `void` Dummy message going to surrounded compartment.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`adjacent`** `void` Dummy message coming from adjacent compartment to current oneImplies that compts are peers: do not surround each other
-**`outside`** `void` Dummy message coming from surrounding compartment to this one.Implies that the originating compartment surrounds this one
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## BufPool
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-**`increment`** `double` Increments mol numbers by specified amount. Can be +ve or -ve
-**`decrement`** `double` Decrements mol numbers by specified amount. Can be +ve or -ve
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## CaConc
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Ca`** `double` Calcium concentration.
-**`CaBasal`** `double` Basal Calcium concentration.
-**`Ca_base`** `double` Basal Calcium concentration, synonym for CaBasal
-**`tau`** `double` Settling time for Ca concentration
-**`B`** `double` Volume scaling factor
-**`thick`** `double` Thickness of Ca shell.
-**`ceiling`** `double` Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.
-**`floor`** `double` Floor value for Ca concentration. If Ca < floor, Ca = floor
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`concOut`** `double` Concentration of Ca in pool
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`current`** `double` Calcium Ion current, due to be converted to conc.
-**`currentFraction`** `double,double` Fraction of total Ion current, that is carried by Ca2+.
-**`increase`** `double` Any input current that increases the concentration.
-**`decrease`** `double` Any input current that decreases the concentration.
-**`basal`** `double` Synonym for assignment of basal conc.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message to receive Process message from scheduler
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ChanBase
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Gbar`** `double` Maximal channel conductance
-**`Ek`** `double` Reversal potential of channel
-**`Gk`** `double` Channel conductance variable
-**`Ik`** `double` Channel current variable
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`permeability`** `double` Conductance term going out to GHK object
-**`IkOut`** `double` Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`Vm`** `double` Handles Vm message coming in from compartment
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message to Goldman-Hodgkin-Katz object
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ChemMesh
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`size`** `double` Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.
-**`numDimensions`** `unsigned int` Number of spatial dimensions of this compartment. Usually 3 or 2
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`meshSplit`** `double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >` Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.
-**`meshStats`** `unsigned int,vector<double>` Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`buildDefaultMesh`** `double,unsigned int` Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.
-**`handleRequestMeshStats`** `void` Handles request from SimManager for mesh stats
-**`handleNodeInfo`** `unsigned int,unsigned int` Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`nodeMeshing`** `void` Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Cinfo
-**Author**: Upi Bhalla
-
-**Description**: Class information object.
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`docs`** `string` Documentation
-**`baseClass`** `string` Name of base class
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Clock
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`runTime`** `double` Duration to run the simulation
-**`currentTime`** `double` Current simulation time
-**`nsteps`** `unsigned int` Number of steps to advance the simulation, in units of the smallest timestep on the clock ticks
-**`numTicks`** `unsigned int` Number of clock ticks
-**`currentStep`** `unsigned int` Current simulation step
-**`dts`** `vector<double>` Utility function returning the dt (timestep) of all ticks.
-**`isRunning`** `bool` Utility function to report if simulation is in progress.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`childTick`** `void` Parent of Tick element
-**`finished`** `void` Signal for completion of run
-**`ack`** `unsigned int,unsigned int` Acknowledgement signal for receipt/completion of function.Goes back to Shell on master node
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`start`** `double` Sets off the simulation for the specified duration
-**`step`** `unsigned int` Sets off the simulation for the specified # of steps
-**`stop`** `void` Halts the simulation, with option to restart seamlessly
-**`setupTick`** `unsigned int,double` Sets up a specific clock tick: args tick#, dt
-**`reinit`** `void` Zeroes out all ticks, starts at t = 0
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`clockControl`** `void` Controls all scheduling aspects of Clock, usually from Shell
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Compartment
-**Author**: Upi Bhalla
-
-**Description**: Compartment object, for branching neuron models.
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Vm`** `double` membrane potential
-**`Cm`** `double` Membrane capacitance
-**`Em`** `double` Resting membrane potential
-**`Im`** `double` Current going through membrane
-**`inject`** `double` Current injection to deliver into compartment
-**`initVm`** `double` Initial value for membrane potential
-**`Rm`** `double` Membrane resistance
-**`Ra`** `double` Axial resistance of compartment
-**`diameter`** `double` Diameter of compartment
-**`length`** `double` Length of compartment
-**`x0`** `double` X coordinate of start of compartment
-**`y0`** `double` Y coordinate of start of compartment
-**`z0`** `double` Z coordinate of start of compartment
-**`x`** `double` x coordinate of end of compartment
-**`y`** `double` y coordinate of end of compartment
-**`z`** `double` z coordinate of end of compartment
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`VmOut`** `double` Sends out Vm value of compartment on each timestep
-**`axialOut`** `double` Sends out Vm value of compartment to adjacent compartments,on each timestep
-**`raxialOut`** `double,double` Sends out Raxial information on each timestep, fields are Ra and Vm
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`injectMsg`** `double` The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
-**`randInject`** `double,double` Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.
-**`injectMsg`** `double` The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
-**`cable`** `void` Message for organizing compartments into groups, calledcables. Doesn't do anything.
-**`process`** `void` Handles 'process' call
-**`reinit`** `void` Handles 'reinit' call
-**`initProc`** `void` Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.
-**`initReinit`** `void` Handles Reinit call for the 'init' phase of the Compartment calculations.
-**`handleChannel`** `double,double` Handles conductance and Reversal potential arguments from Channel
-**`handleRaxial`** `double,double` Handles Raxial info: arguments are Ra and Vm.
-**`handleAxial`** `double` Handles Axial information. Argument is just Vm.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` This is a shared message to receive Process messages from the scheduler objects. The Process should be called _second_ in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-**`init`** `void` This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.
-**`channel`** `void` This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm
-**`axial`** `void` This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.
-**`raxial`** `void` This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## CplxEnzBase
-**Author**: Upi Bhalla
-
-**Description**:: Base class for mass-action enzymes in which there is an explicit pool for the enzyme-substrate complex. It models the reaction: E + S <===> E.S ----> E + P
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Km`** `double` Michaelis-Menten constant in SI conc units (milliMolar)
-**`numKm`** `double` Michaelis-Menten constant in number units, volume dependent
-**`kcat`** `double` Forward rate constant for enzyme, units 1/sec
-**`numSubstrates`** `unsigned int` Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
-**`k1`** `double` Forward reaction from enz + sub to complex
-**`k2`** `double` Reverse reaction from complex to enz + sub
-**`k3`** `double` Forward rate constant from complex to product + enz
-**`ratio`** `double` Ratio of k2/k3
-**`concK1`** `double` K1 expressed in concentration (1/millimolar.sec) units
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-**`toEnz`** `double,double` Sends out increment of molecules on product each timestep
-**`toCplx`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product. Dummy.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the MMEnz to recompute its numKm after remeshing
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`cplxDest`** `double` Handles # of molecules of enz-sub complex
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate molecule
-**`prd`** `void` Connects to product molecule
-**`proc`** `void` Shared message for process and reinit
-**`enz`** `void` Connects to enzyme pool
-**`cplx`** `void` Connects to enz-sub complex pool
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## CubeMesh
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`size`** `double` Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.
-**`numDimensions`** `unsigned int` Number of spatial dimensions of this compartment. Usually 3 or 2
-**`isToroid`** `bool` Flag. True when the mesh should be toroidal, that is,when going beyond the right face brings us around to theleft-most mesh entry, and so on. If we have nx, ny, nzentries, this rule means that the coordinate (x, ny, z)will map onto (x, 0, z). Similarly,(-1, y, z) -> (nx-1, y, z)Default is false
-**`preserveNumEntries`** `bool` Flag. When it is true, the numbers nx, ny, nz remainunchanged when x0, x1, y0, y1, z0, z1 are altered. Thusdx, dy, dz would change instead. When it is false, thendx, dy, dz remain the same and nx, ny, nz are altered.Default is true
-**`x0`** `double` X coord of one end
-**`y0`** `double` Y coord of one end
-**`z0`** `double` Z coord of one end
-**`x1`** `double` X coord of other end
-**`y1`** `double` Y coord of other end
-**`z1`** `double` Z coord of other end
-**`dx`** `double` X size for mesh
-**`dy`** `double` Y size for mesh
-**`dz`** `double` Z size for mesh
-**`nx`** `unsigned int` Number of subdivisions in mesh in X
-**`ny`** `unsigned int` Number of subdivisions in mesh in Y
-**`nz`** `unsigned int` Number of subdivisions in mesh in Z
-**`coords`** `vector<double>` Set all the coords of the cuboid at once. Order is:x0 y0 z0 x1 y1 z1 dx dy dz
-**`meshToSpace`** `vector<unsigned int>` Array in which each mesh entry stores spatial (cubic) index
-**`spaceToMesh`** `vector<unsigned int>` Array in which each space index (obtained by linearizing the xyz coords) specifies which meshIndex is present.In many cases the index will store the EMPTY flag if there isno mesh entry at that spatial location
-**`surface`** `vector<unsigned int>` Array specifying surface of arbitrary volume within the CubeMesh. All entries must fall within the cuboid. Each entry of the array is a spatial index obtained by linearizing the ix, iy, iz coordinates within the cuboid. So, each entry == ( iz * ny + iy ) * nx + ixNote that the voxels listed on the surface are WITHIN the volume of the CubeMesh object
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`meshSplit`** `double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >` Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.
-**`meshStats`** `unsigned int,vector<double>` Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`buildDefaultMesh`** `double,unsigned int` Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.
-**`handleRequestMeshStats`** `void` Handles request from SimManager for mesh stats
-**`handleNodeInfo`** `unsigned int,unsigned int` Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`nodeMeshing`** `void` Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## CylMesh
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`size`** `double` Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.
-**`numDimensions`** `unsigned int` Number of spatial dimensions of this compartment. Usually 3 or 2
-**`x0`** `double` x coord of one end
-**`y0`** `double` y coord of one end
-**`z0`** `double` z coord of one end
-**`r0`** `double` Radius of one end
-**`x1`** `double` x coord of other end
-**`y1`** `double` y coord of other end
-**`z1`** `double` z coord of other end
-**`r1`** `double` Radius of other end
-**`lambda`** `double` Length constant to use for subdivisionsThe system will attempt to subdivide using compartments oflength lambda on average. If the cylinder has different enddiameters r0 and r1, it will scale to smaller lengthsfor the smaller diameter end and vice versa.Once the value is set it will recompute lambda as totLength/numEntries
-**`coords`** `vector<double>` All the coords as a single vector: x0 y0 z0 x1 y1 z1 r0 r1 lambda
-**`totLength`** `double` Total length of cylinder
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`meshSplit`** `double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >` Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.
-**`meshStats`** `unsigned int,vector<double>` Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`buildDefaultMesh`** `double,unsigned int` Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.
-**`handleRequestMeshStats`** `void` Handles request from SimManager for mesh stats
-**`handleNodeInfo`** `unsigned int,unsigned int` Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`nodeMeshing`** `void` Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## CylPanel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`nPts`** `unsigned int` Number of points used by panel to specify geometry
-**`nDims`** `unsigned int` Number of Dimensions used by panel to specify geometry
-**`numNeighbors`** `unsigned int` Number of Neighbors of panel
-**`shapeId`** `unsigned int` Identifier for shape type, as used by Smoldyn
-**`coords`** `vector<double>` All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toNeighbor`** `void` Identifies neighbors of the current panel
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`neighbor`** `void` Handles incoming message from neighbor
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`x`** `unsigned int,double` x coordinate identified by index
-**`y`** `unsigned int,double` y coordinate identified by index
-**`z`** `unsigned int,double` z coordinate identified by index
-
-
-## DiagonalMsg
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`e1`** `Id` Id of source Element.
-**`e2`** `Id` Id of source Element.
-**`srcFieldsOnE1`** `vector<string>` Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector
-**`destFieldsOnE2`** `vector<string>` Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector
-**`srcFieldsOnE2`** `vector<string>` Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector
-**`destFieldsOnE1`** `vector<string>` Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
-**`stride`** `int` The stride is the increment to the src DataId that gives thedest DataId. It can be positive or negative, but bounds checkingtakes place and it does not wrap around.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## DiffAmp
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`gain`** `double` Gain of the amplifier. The output of the amplifier is the difference between the totals in plus and minus inputs multiplied by the gain. Defaults to 1
-**`saturation`** `double` Saturation is the bound on the output. If output goes beyond the +/-saturation range, it is truncated to the closer of +saturation and -saturation. Defaults to the maximum double precision floating point number representable on the system.
-**`output`** `double` Output of the amplifier, i.e. gain * (plus - minus).
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`outputOut`** `double` Current output level.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`gainIn`** `double` Destination message to control gain dynamically.
-**`plusIn`** `double` Positive input terminal of the amplifier. All the messages connected here are summed up to get total positive input.
-**`minusIn`** `double` Negative input terminal of the amplifier. All the messages connected here are summed up to get total positive input.
-**`process`** `void` Handles process call, updates internal time stamp.
-**`reinit`** `void` Handles reinit call.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## DiskPanel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`nPts`** `unsigned int` Number of points used by panel to specify geometry
-**`nDims`** `unsigned int` Number of Dimensions used by panel to specify geometry
-**`numNeighbors`** `unsigned int` Number of Neighbors of panel
-**`shapeId`** `unsigned int` Identifier for shape type, as used by Smoldyn
-**`coords`** `vector<double>` All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toNeighbor`** `void` Identifies neighbors of the current panel
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`neighbor`** `void` Handles incoming message from neighbor
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`x`** `unsigned int,double` x coordinate identified by index
-**`y`** `unsigned int,double` y coordinate identified by index
-**`z`** `unsigned int,double` z coordinate identified by index
-
-
-## Enz
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Km`** `double` Michaelis-Menten constant in SI conc units (milliMolar)
-**`numKm`** `double` Michaelis-Menten constant in number units, volume dependent
-**`kcat`** `double` Forward rate constant for enzyme, units 1/sec
-**`numSubstrates`** `unsigned int` Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
-**`k1`** `double` Forward reaction from enz + sub to complex
-**`k2`** `double` Reverse reaction from complex to enz + sub
-**`k3`** `double` Forward rate constant from complex to product + enz
-**`ratio`** `double` Ratio of k2/k3
-**`concK1`** `double` K1 expressed in concentration (1/millimolar.sec) units
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-**`toEnz`** `double,double` Sends out increment of molecules on product each timestep
-**`toCplx`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product. Dummy.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the MMEnz to recompute its numKm after remeshing
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`cplxDest`** `double` Handles # of molecules of enz-sub complex
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate molecule
-**`prd`** `void` Connects to product molecule
-**`proc`** `void` Shared message for process and reinit
-**`enz`** `void` Connects to enzyme pool
-**`cplx`** `void` Connects to enz-sub complex pool
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## EnzBase
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Km`** `double` Michaelis-Menten constant in SI conc units (milliMolar)
-**`numKm`** `double` Michaelis-Menten constant in number units, volume dependent
-**`kcat`** `double` Forward rate constant for enzyme, units 1/sec
-**`numSubstrates`** `unsigned int` Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product. Dummy.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the MMEnz to recompute its numKm after remeshing
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate molecule
-**`prd`** `void` Connects to product molecule
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Finfo
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`name`** `string` Name of Finfo
-**`docs`** `string` Documentation for Finfo
-**`type`** `string` RTTI type info for this Finfo
-**`src`** `vector<string>` Subsidiary SrcFinfos. Useful for SharedFinfos
-**`dest`** `vector<string>` Subsidiary DestFinfos. Useful for SharedFinfos
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## FuncBase
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`result`** `double` Outcome of function computation
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`output`** `double` Sends out sum on each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`input`** `double` Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## FuncPool
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-**`increment`** `double` Increments mol numbers by specified amount. Can be +ve or -ve
-**`decrement`** `double` Decrements mol numbers by specified amount. Can be +ve or -ve
-**`input`** `double` Handles input to control value of n_
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## GHK
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Ik`** `double` Membrane current
-**`Gk`** `double` Conductance
-**`Ek`** `double` Reversal Potential
-**`T`** `double` Temperature of system
-**`p`** `double` Permeability of channel
-**`Vm`** `double` Membrane potential
-**`Cin`** `double` Internal concentration
-**`Cout`** `double` External ion concentration
-**`valency`** `double` Valence of ion
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`VmOut`** `double` Relay of membrane potential Vm.
-**`IkOut`** `double` MembraneCurrent.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`process`** `void` Handles process call
-**`handleVm`** `double` Handles Vm message coming in from compartment
-**`addPermeability`** `double` Handles permeability message coming in from channel
-**`CinDest`** `double` Alias for set_Cin
-**`CoutDest`** `double` Alias for set_Cout
-**`addPermeability`** `double` Handles permeability message coming in from channel
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message from channel to current Goldman-Hodgkin-Katz objectThis shared message connects to an HHChannel. The first entry is a MsgSrc which relays the Vm received from a compartment. The second entry is a MsgDest which receives channel conductance, and interprets it as permeability.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Geometry
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`epsilon`** `double` epsilon is the max deviation of surface-point from surface.I think it refers to when the molecule is stuck to the surface. Need to check with Steven.
-**`neighdist`** `double` neighdist is capture distance from one panel to another.When a molecule diffuses off one panel and is within neighdist of the other, it is captured by the second.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`returnSize`** `double` Return size of compartment
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`handleSizeRequest`** `void` Handles a request for size. Part of SharedMsg to ChemCompt.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`compt`** `void` Connects to compartment(s) to specify geometry.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Group
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`group`** `void` Handle for grouping Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## GslIntegrator
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`isInitialized`** `bool` True if the Stoich message has come in to set parms
-**`method`** `string` Numerical method to use.
-**`relativeAccuracy`** `double` Accuracy criterion
-**`absoluteAccuracy`** `double` Another accuracy criterion
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`stoich`** `Id` Handle data from Stoich
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## GslStoich
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`isInitialized`** `bool` True if the Stoich message has come in to set parms
-**`method`** `string` Numerical method to use.
-**`relativeAccuracy`** `double` Accuracy criterion
-**`absoluteAccuracy`** `double` Another accuracy criterion
-**`compartment`** `Id` This is the Id of the compartment, which must be derived fromthe ChemMesh baseclass. The GslStoich needsthe ChemMesh Id only for diffusion, and one can pass in Id() instead if there is no diffusion, or just leave it unset.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`addJunction`** `Id` Add a junction between the current solver and the one whose Id is passed in.
-**`dropJunction`** `Id` Drops a junction between the current solver and the one whose Id is passed in. Ignores if no junction.
-**`stoich`** `Id` Assign the StoichCore and ChemMesh Ids. The GslStoich needsthe StoichCore pointer in all cases, in order to perform allcalculations.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`initProc`** `void` Handles init call
-**`initReinit`** `void` Handles initReinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-**`init`** `void` Shared message for init and initReinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## GssaStoich
-**Author**: Upinder S. Bhalla, 2008, 2011, NCBS
-
-**Description**: GssaStoich: Gillespie Stochastic Simulation Algorithm object.Closely based on the Stoich object and inherits its handling functions for constructing the matrix. Sets up stoichiometry matrix based calculations from a
-
-wildcard path for the reaction system.Knows how to compute derivatives for most common things, also knows how to handle special cases where the object will have to do its own computation.Generates a stoichiometry matrix, which is useful for lots of other operations as well.
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`useOneWayReacs`** `bool` Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations
-**`nVarPools`** `unsigned int` Number of variable molecule pools in the reac system
-**`numMeshEntries`** `unsigned int` Number of meshEntries in reac-diff system
-**`estimatedDt`** `double` Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.
-**`path`** `string` Path of reaction system to take over
-**`path`** `string` Path of reaction system to take over and solve
-**`method`** `string` Numerical method to use for the GssaStoich. The defaultand currently the only method is Gillespie1.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`plugin`** `Id` Sends out Stoich Id so that plugins can directly access fields and functions
-**`nodeDiffBoundary`** `unsigned int,vector<unsigned int>,vector<double>` Sends mol #s across boundary between nodes, to calculate diffusionterms. arg1 is originating node, arg2 is list of meshIndices forwhich data is being transferred, and arg3 are the 'n' values forall the pools on the specified meshIndices, to be plugged intothe appropriate place on the recipient node's S_ matrix
-**`poolsReactingAcrossBoundary`** `unsigned int,vector<double>` A vector of mol counts (n) of those pools that react across a boundary. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.
-**`reacRollbacksAcrossBoundary`** `unsigned int,vector<double>` Occasionally, a Gillespie advance will cause the mol conc on the target stoich side to become negative. If so, this message does a patch up job by telling the originating Stoich to roll back to the specified number of reac firings, which is the max that the target was able to handle. This is probably numerically naughty, but it is better than negative concentrations
-**`reacRatesAcrossBoundary`** `unsigned int,vector<double>` A vector of reac rates (V) of each reaction crossing the boundary between compartments. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. In the case of Gillespie calculations *V* is the integer # of transitions (firings) of each reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`meshSplit`** `double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >` Handles message from ChemMesh that defines how meshEntries are decomposed on this node, and how they communicate between nodes.Args: (oldVol, volumeVectorForAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#])
-**`handleReacRatesAcrossBoundary`** `unsigned int,vector<double>` When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.
-**`handlePoolsReactingAcrossBoundary`** `unsigned int,vector<double>` When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of pool #s for every pool that reacts across the boundary, in every mesh entry. that reacts across a boundary, in every mesh entry
-**`handleReacRollbacksAcrossBoundary`** `unsigned int,vector<double>` When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. Only one side does the calculations to assure mass conservation. There are rare cases when the calculations of one solver, typically a Gillespie one, gives such a large change that the concentrations on the other side would become negative in one or more molecules This message handles such cases on the Gillespie side, by telling the solver to roll back its recent calculation and instead use the specified vector for the rates, that is the # of mols changed in the latest timestep. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinint call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`boundaryReacOut`** `void` Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.
-**`boundaryReacIn`** `void` Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## HDF5DataWriter
-**Author**: Subhasis Ray
-
-**Description**: HDF5 file writer for saving data tables. It saves the tables connected to it via `requestData` field into an HDF5 file. The path of the table is maintained in the HDF5 file, with a HDF5 group for each element above the table.
-
-Thus, if you have a table `/data/VmTable` in MOOSE, then it will be written as an HDF5 table called `VmTable` inside an HDF5 Group called `data`.
-
-However Table inside Table is considered a pathological case and is not handled.
-
-At every process call it writes the contents of the tables to the file and clears the table vectors. You can explicitly force writing of the data via the `flush` function.
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`filename`** `string` Name of the file associated with this HDF5 writer object.
-**`isOpen`** `bool` True if this object has an open file handle.
-**`mode`** `unsigned int` Depending on mode, if file already exists, if mode=1, data will be appended to existing file, if mode=2, file will be truncated, if mode=4, no writing will happen.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`requestData`** `unsigned int` Sends request for a field to target object
-**`clear`** `void` Send request to clear a Table vector.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`flush`** `void` Write all buffer contents to file and clear the buffers.
-**`recvData`** `bad` Handles data sent back following request
-**`process`** `void` Handle process calls. Write data to file and clear all Table objects associated with this. Hence you want to keep it on a slow clock 1000 times or more slower than that for the tables.
-**`reinit`** `void` Reinitialize the object. If the current file handle is valid, it tries to close that and open the file specified in current filename field.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message to receive process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## HDF5WriterBase
-**Author**: Subhasis Ray
-
-**Description**: HDF5 file writer base class. This is not to be used directly. Instead, it should be subclassed to provide specific data writing functions. This class provides most basic properties like filename, file opening mode, file open status.
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`filename`** `string` Name of the file associated with this HDF5 writer object.
-**`isOpen`** `bool` True if this object has an open file handle.
-**`mode`** `unsigned int` Depending on mode, if file already exists, if mode=1, data will be appended to existing file, if mode=2, file will be truncated, if mode=4, no writing will happen.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`flush`** `void` Write all buffer contents to file and clear the buffers.
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## HHChannel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Gbar`** `double` Maximal channel conductance
-**`Ek`** `double` Reversal potential of channel
-**`Gk`** `double` Channel conductance variable
-**`Ik`** `double` Channel current variable
-**`Xpower`** `double` Power for X gate
-**`Ypower`** `double` Power for Y gate
-**`Zpower`** `double` Power for Z gate
-**`instant`** `int` Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state
-**`X`** `double` State variable for X gate
-**`Y`** `double` State variable for Y gate
-**`Z`** `double` State variable for Y gate
-**`useConcentration`** `int` Flag: when true, use concentration message rather than Vm tocontrol Z gate
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`permeability`** `double` Conductance term going out to GHK object
-**`IkOut`** `double` Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`concen`** `double` Incoming message from Concen object to specific conc to usein the Z gate calculations
-**`createGate`** `string` Function to create specified gate.Argument: Gate type [X Y Z]
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message to Goldman-Hodgkin-Katz object
-**`proc`** `void` This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.
- The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## HHChannel2D
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Gbar`** `double` Maximal channel conductance
-**`Ek`** `double` Reversal potential of channel
-**`Gk`** `double` Channel conductance variable
-**`Ik`** `double` Channel current variable
-**`Xindex`** `string` String for setting X index.
-**`Yindex`** `string` String for setting Y index.
-**`Zindex`** `string` String for setting Z index.
-**`Xpower`** `double` Power for X gate
-**`Ypower`** `double` Power for Y gate
-**`Zpower`** `double` Power for Z gate
-**`instant`** `int` Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state
-**`X`** `double` State variable for X gate
-**`Y`** `double` State variable for Y gate
-**`Z`** `double` State variable for Y gate
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`permeability`** `double` Conductance term going out to GHK object
-**`IkOut`** `double` Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`concen`** `double` Incoming message from Concen object to specific conc to useas the first concen variable
-**`concen2`** `double` Incoming message from Concen object to specific conc to useas the second concen variable
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message to Goldman-Hodgkin-Katz object
-**`proc`** `void` This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.
- The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## HHGate
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`alpha`** `vector<double>` Parameters for voltage-dependent rates, alpha:Set up alpha term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
-**`beta`** `vector<double>` Parameters for voltage-dependent rates, beta:Set up beta term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
-**`tau`** `vector<double>` Parameters for voltage-dependent rates, tau:Set up tau curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))
-**`mInfinity`** `vector<double>` Parameters for voltage-dependent rates, mInfinity:Set up mInfinity curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
-**`min`** `double` Minimum range for lookup
-**`max`** `double` Minimum range for lookup
-**`divs`** `unsigned int` Divisions for lookup. Zero means to use linear interpolation
-**`tableA`** `vector<double>` Table of A entries
-**`tableB`** `vector<double>` Table of alpha + beta entries
-**`useInterpolation`** `bool` Flag: use linear interpolation if true, else direct lookup
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`setupAlpha`** `vector<double>` Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
-**`setupTau`** `vector<double>` Identical to setupAlpha, except that the forms specified bythe 13 parameters are for the tau and m-infinity curves ratherthan the alpha and beta terms. So the parameters are:setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmaxAs before, the equation describing each curve is:y(x) = (A + B * x) / (C + exp((x + D) / F))
-**`tweakAlpha`** `void` Dummy function for backward compatibility. It used to convertthe tables from alpha, beta values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.
-**`tweakTau`** `void` Dummy function for backward compatibility. It used to convertthe tables from tau, minf values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.
-**`setupGate`** `vector<double>` Sets up one gate at a time using the alpha/beta form.Has 9 parameters, as follows:setupGate A B C D F xdivs xmin xmax is_betaThis sets up the gate using the equation:y(x) = (A + B * x) / (C + exp((x + D) / F))Deprecated.
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`A`** `double,double` lookupA: Look up the A gate value from a double. Usually doesso by direct scaling and offset to an integer lookup, usinga fine enough table granularity that there is little error.Alternatively uses linear interpolation.The range of the double is predefined based on knowledge ofvoltage or conc ranges, and the granularity is specified bythe xmin, xmax, and dV fields.
-**`B`** `double,double` lookupB: Look up the B gate value from a double.Note that this looks up the raw tables, which are transformedfrom the reference parameters.
-
-
-## HHGate2D
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`A`** `vector<double>,double` lookupA: Look up the A gate value from two doubles, passedin as a vector. Uses linear interpolation in the 2D tableThe range of the lookup doubles is predefined based on knowledge of voltage or conc ranges, and the granularity is specified by the xmin, xmax, and dx field, and their y-axis counterparts.
-**`B`** `vector<double>,double` lookupB: Look up B gate value from two doubles in a vector.
-
-
-## HSolve
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`seed`** `Id` Use this field to specify path to a 'seed' compartment, that is, any compartment within a neuron. The HSolve object uses this seed as a handle to discover the rest of the neuronal model, which means all the remaining compartments, channels, synapses, etc.
-**`target`** `string` Specifies the path to a compartmental model to be taken over. This can be the path to any container object that has the model under it (found by performing a deep search). Alternatively, this can also be the path to any compartment within the neuron. This compartment will be used as a handle to discover the rest of the model, which means all the remaining compartments, channels, synapses, etc.
-**`dt`** `double` The time-step for this solver.
-**`caAdvance`** `int` This flag determines how current flowing into a calcium pool is computed. A value of 0 means that the membrane potential at the beginning of the time-step is used for the calculation. This is how GENESIS does its computations. A value of 1 means the membrane potential at the middle of the time-step is used. This is the correct way of integration, and is the default way.
-**`vDiv`** `int` Specifies number of divisions for lookup tables of voltage-sensitive channels.
-**`vMin`** `double` Specifies the lower bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
-**`vMax`** `double` Specifies the upper bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
-**`caDiv`** `int` Specifies number of divisions for lookup tables of calcium-sensitive channels.
-**`caMin`** `double` Specifies the lower bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
-**`caMax`** `double` Specifies the upper bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`process`** `void` Handles 'process' call: Solver advances by one time-step.
-**`reinit`** `void` Handles 'reinit' call: Solver reads in model.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Handles 'reinit' and 'process' calls from a clock.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## HemispherePanel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`nPts`** `unsigned int` Number of points used by panel to specify geometry
-**`nDims`** `unsigned int` Number of Dimensions used by panel to specify geometry
-**`numNeighbors`** `unsigned int` Number of Neighbors of panel
-**`shapeId`** `unsigned int` Identifier for shape type, as used by Smoldyn
-**`coords`** `vector<double>` All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toNeighbor`** `void` Identifies neighbors of the current panel
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`neighbor`** `void` Handles incoming message from neighbor
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`x`** `unsigned int,double` x coordinate identified by index
-**`y`** `unsigned int,double` y coordinate identified by index
-**`z`** `unsigned int,double` z coordinate identified by index
-
-
-## IntFire
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`numSynapses`** `unsigned int` Number of synapses on SynBase
-**`Vm`** `double` Membrane potential
-**`tau`** `double` charging time-course
-**`thresh`** `double` firing threshold
-**`refractoryPeriod`** `double` Minimum time between successive spikes
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`spike`** `double` Sends out spike events
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Interpol2D
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`xmin`** `double` Minimum value for x axis of lookup table
-**`xmax`** `double` Maximum value for x axis of lookup table
-**`xdivs`** `unsigned int` # of divisions on x axis of lookup table
-**`dx`** `double` Increment on x axis of lookup table
-**`ymin`** `double` Minimum value for y axis of lookup table
-**`ymax`** `double` Maximum value for y axis of lookup table
-**`ydivs`** `unsigned int` # of divisions on y axis of lookup table
-**`dy`** `double` Increment on y axis of lookup table
-**`tableVector2D`** `vector< vector<double> >` Get the entire table.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`trig`** `double` respond to a request for a value lookup
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`lookup`** `double,double` Looks up table value based on indices v1 and v2, and sendsvalue back using the 'trig' message
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`lookupReturn2D`** `void` This is a shared message for doing lookups on the table. Receives 2 doubles: x, y. Sends back a double with the looked-up z value.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`table`** `vector<unsigned int>,double` Lookup an entry on the table
-**`z`** `vector<double>,double` Interpolated value for specified x and y. This is provided for debugging. Normally other objects will retrieve interpolated values via lookup message.
-
-
-## IzhikevichNrn
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Vmax`** `double` Maximum membrane potential. Membrane potential is reset to c whenever it reaches Vmax. NOTE: Izhikevich model specifies the PEAK voltage, rather than THRSHOLD voltage. The threshold depends on the previous history.
-**`c`** `double` Reset potential. Membrane potential is reset to c whenever it reaches Vmax.
-**`d`** `double` Parameter d in Izhikevich model. Unit is V/s.
-**`a`** `double` Parameter a in Izhikevich model. Unit is s^{-1}
-**`b`** `double` Parameter b in Izhikevich model. Unit is s^{-1}
-**`u`** `double` Parameter u in Izhikevich equation. Unit is V/s
-**`Vm`** `double` Membrane potential, equivalent to v in Izhikevich equation.
-**`Im`** `double` Total current going through the membrane. Unit is A.
-**`Rm`** `double` Hidden cefficient of input current term (I) in Izhikevich model. Defaults to 1e6 Ohm.
-**`initVm`** `double` Initial membrane potential. Unit is V.
-**`initU`** `double` Initial value of u.
-**`alpha`** `double` Coefficient of v^2 in Izhikevich equation. Defaults to 0.04 in physiological unit. In SI it should be 40000.0. Unit is V^-1 s^{-1}
-**`beta`** `double` Coefficient of v in Izhikevich model. Defaults to 5 in physiological unit, 5000.0 for SI units. Unit is s^{-1}
-**`gamma`** `double` Constant term in Izhikevich model. Defaults to 140 in both physiological and SI units. unit is V/s.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`VmOut`** `double` Sends out Vm
-**`spike`** `double` Sends out spike events
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`injectDest`** `double` Injection current into the neuron.
-**`cDest`** `double` Destination message to modify parameter c at runtime.
-**`dDest`** `double` Destination message to modify parameter d at runtime.
-**`bDest`** `double` Destination message to modify parameter b at runtime
-**`aDest`** `double` Destination message modify parameter a at runtime.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message to receive Process message from scheduler
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## LeakyIaF
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Cm`** `double` Membrane capacitance.
-**`Rm`** `double` Membrane resistance, inverse of leak-conductance.
-**`Em`** `double` Leak reversal potential
-**`Vm`** `double` Membrane potential
-**`initVm`** `double` Inital value of membrane potential
-**`Vreset`** `double` Reset potnetial after firing.
-**`Vthreshold`** `double` firing threshold
-**`refractoryPeriod`** `double` Minimum time between successive spikes
-**`inject`** `double` Injection current.
-**`tSpike`** `double` Time of the last spike
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`spike`** `double` Sends out spike events
-**`VmOut`** `double` Sends out Vm
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`injectDest`** `double` Destination for current input.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## MMenz
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Km`** `double` Michaelis-Menten constant in SI conc units (milliMolar)
-**`numKm`** `double` Michaelis-Menten constant in number units, volume dependent
-**`kcat`** `double` Forward rate constant for enzyme, units 1/sec
-**`numSubstrates`** `unsigned int` Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product. Dummy.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the MMEnz to recompute its numKm after remeshing
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate molecule
-**`prd`** `void` Connects to product molecule
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## MarkovChannel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Gbar`** `double` Maximal channel conductance
-**`Ek`** `double` Reversal potential of channel
-**`Gk`** `double` Channel conductance variable
-**`Ik`** `double` Channel current variable
-**`ligandconc`** `double` Ligand concentration.
-**`vm`** `double` Membrane voltage.
-**`numstates`** `unsigned int` The number of states that the channel can occupy.
-**`numopenstates`** `unsigned int` The number of states which are open/conducting.
-**`state`** `vector<double>` This is a row vector that contains the probabilities of finding the channel in each state.
-**`initialstate`** `vector<double>` This is a row vector that contains the probabilities of finding the channel in each state at t = 0. The state of the channel is reset to this value during a call to reinit()
-**`labels`** `vector<string>` Labels for each state.
-**`gbar`** `vector<double>` A row vector containing the conductance associated with each of the open/conducting states.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`permeability`** `double` Conductance term going out to GHK object
-**`IkOut`** `double` Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleligandconc`** `double` Deals with incoming messages containing information of ligand concentration
-**`handlestate`** `vector<double>` Deals with incoming message from MarkovSolver object containing state information of the channel.
-
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message to Goldman-Hodgkin-Katz object
-**`proc`** `void` This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## MarkovGslSolver
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`isInitialized`** `bool` True if the message has come in to set solver parameters.
-**`method`** `string` Numerical method to use.
-**`relativeAccuracy`** `double` Accuracy criterion
-**`absoluteAccuracy`** `double` Another accuracy criterion
-**`internalDt`** `double` internal timestep to use.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`stateOut`** `vector<double>` Sends updated state to the MarkovChannel class.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`init`** `vector<double>` Initialize solver parameters.
-**`handleQ`** `vector< vector<double> >` Handles information regarding the instantaneous rate matrix from the MarkovRateTable class.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## MarkovRateTable
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`vm`** `double` Membrane voltage.
-**`ligandconc`** `double` Ligand concentration.
-**`Q`** `vector< vector<double> >` Instantaneous rate matrix.
-**`size`** `unsigned int` Dimension of the families of lookup tables. Is always equal to the number of states in the model.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`instratesOut`** `vector< vector<double> >` Sends out instantaneous rate information of varying transition rates at each time step.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`handleVm`** `double` Handles incoming message containing voltage information.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`init`** `unsigned int` Initialization of the class. Allocates memory for all the tables.
-**`handleLigandConc`** `double` Handles incoming message containing ligand concentration.
-**`set1d`** `unsigned int,unsigned int,Id,unsigned int` Setting up of 1D lookup table for the (i,j)'th rate.
-**`set2d`** `unsigned int,unsigned int,Id` Setting up of 2D lookup table for the (i,j)'th rate.
-**`setconst`** `unsigned int,unsigned int,double` Setting a constant value for the (i,j)'th rate. Internally, this is stored as a 1-D rate with a lookup table containing 1 entry.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This message couples the rate table to the compartment. The rate table needs updates on voltage in order to compute the rate table.
-**`proc`** `void` This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## MarkovSolver
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Q`** `vector< vector<double> >` Instantaneous rate matrix.
-**`state`** `vector<double>` Current state of the channel.
-**`initialstate`** `vector<double>` Initial state of the channel.
-**`xmin`** `double` Minimum value for x axis of lookup table
-**`xmax`** `double` Maximum value for x axis of lookup table
-**`xdivs`** `unsigned int` # of divisions on x axis of lookup table
-**`invdx`** `double` Reciprocal of increment on x axis of lookup table
-**`ymin`** `double` Minimum value for y axis of lookup table
-**`ymax`** `double` Maximum value for y axis of lookup table
-**`ydivs`** `unsigned int` # of divisions on y axis of lookup table
-**`invdy`** `double` Reciprocal of increment on y axis of lookup table
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`stateOut`** `vector<double>` Sends updated state to the MarkovChannel class.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`handleVm`** `double` Handles incoming message containing voltage information.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`ligandconc`** `double` Handles incoming message containing ligand concentration.
-**`init`** `Id,double` Setups the table of matrix exponentials associated with the solver object.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.
-**`proc`** `void` This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-**`proc`** `void` This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## MarkovSolverBase
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Q`** `vector< vector<double> >` Instantaneous rate matrix.
-**`state`** `vector<double>` Current state of the channel.
-**`initialstate`** `vector<double>` Initial state of the channel.
-**`xmin`** `double` Minimum value for x axis of lookup table
-**`xmax`** `double` Maximum value for x axis of lookup table
-**`xdivs`** `unsigned int` # of divisions on x axis of lookup table
-**`invdx`** `double` Reciprocal of increment on x axis of lookup table
-**`ymin`** `double` Minimum value for y axis of lookup table
-**`ymax`** `double` Maximum value for y axis of lookup table
-**`ydivs`** `unsigned int` # of divisions on y axis of lookup table
-**`invdy`** `double` Reciprocal of increment on y axis of lookup table
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`stateOut`** `vector<double>` Sends updated state to the MarkovChannel class.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`handleVm`** `double` Handles incoming message containing voltage information.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`ligandconc`** `double` Handles incoming message containing ligand concentration.
-**`init`** `Id,double` Setups the table of matrix exponentials associated with the solver object.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.
-**`proc`** `void` This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## MathFunc
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`mathML`** `string` MathML version of expression to compute
-**`function`** `string` function is for functions of form f(x, y) = x + y
-**`result`** `double` result value
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`output`** `double` Sends out result of computation
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`arg1`** `double` Handle arg1
-**`arg2`** `double` Handle arg2
-**`arg3`** `double` Handle arg3
-**`arg4`** `double` Handle arg4
-**`process`** `void` Handle process call
-**`reinit`** `void` Handle reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Mdouble
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`this`** `double` Access function for entire Mdouble object.
-**`value`** `double` Access function for value field of Mdouble object,which happens also to be the entire contents of the object.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## MeshEntry
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`size`** `double` Volume of this MeshEntry
-**`dimensions`** `unsigned int` number of dimensions of this MeshEntry
-**`meshType`** `unsigned int` The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder 3. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral
-**`Coordinates`** `vector<double>` Coordinates that define current MeshEntry. Depend on MeshType.
-**`neighbors`** `vector<unsigned int>` Indices of other MeshEntries that this one connects to
-**`DiffusionArea`** `vector<double>` Diffusion area for geometry of interface
-**`DiffusionScaling`** `vector<double>` Diffusion scaling for geometry of interface
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Tells the target pool or other entity that the compartment subdivision(meshing) has changed, and that it has to redo its volume and memory allocation accordingly.Arguments are: oldvol, numTotalEntries, startEntry, localIndices, volsThe vols specifies volumes of each local mesh entry. It also specifieshow many meshEntries are present on the local node.The localIndices vector is used for general load balancing only.It has a list of the all meshEntries on current node.If it is empty, we assume block load balancing. In this secondcase the contents of the current node go from startEntry to startEntry + vols.size().
-**`remeshReacs`** `void` Tells connected enz or reac that the compartment subdivision(meshing) has changed, and that it has to redo its volume-dependent rate terms like numKf_ accordingly.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-**`mesh`** `void` Shared message for updating mesh volumes and subdivisions,typically controls pool sizes
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## MgBlock
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Gbar`** `double` Maximal channel conductance
-**`Ek`** `double` Reversal potential of channel
-**`Gk`** `double` Channel conductance variable
-**`Ik`** `double` Channel current variable
-**`KMg_A`** `double` 1/eta
-**`KMg_B`** `double` 1/gamma
-**`CMg`** `double` [Mg] in mM
-**`Ik`** `double` Current through MgBlock
-**`Zk`** `double` Charge on ion
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`permeability`** `double` Conductance term going out to GHK object
-**`IkOut`** `double` Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`process`** `void` Handles process call
-**`origChannel`** `double,double`
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message to Goldman-Hodgkin-Katz object
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Msg
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`e1`** `Id` Id of source Element.
-**`e2`** `Id` Id of source Element.
-**`srcFieldsOnE1`** `vector<string>` Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector
-**`destFieldsOnE2`** `vector<string>` Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector
-**`srcFieldsOnE2`** `vector<string>` Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector
-**`destFieldsOnE1`** `vector<string>` Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Mstring
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`this`** `string` Access function for entire Mstring object.
-**`value`** `string` Access function for value field of Mstring object,which happens also to be the entire contents of the object.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## NMDAChan
-**Author**: Subhasis Ray, 2010, NCBS
-
-**Description**: NMDAChan: Extracellular [Mg2+] dependent NMDA channel.This channel has four states as described by Jahr and Stevens (J. Neurosci. 1990, 10(9)) This implementation is based on equation 4(a) in that article. The channel conductance is defined as : k * g(V, [Mg2+]o) * S(t) where k is a scaling constant. S(t) is the legand gated component of the conductance. It rises linearly for t = tau2. Then decays exponentially with time constant t = tau1. g is a function of voltage and the extracellular [Mg2+] defined as: 1 / { 1 + (a1 + a2) * (a1 * B1 + a2 * B2)/ [A * a1 * (b1 + B1) + A * a2 * (b2 + B2)]}
-
-a1 = 1e3 * exp( - c0 * V - c1) s^{-1}, c0 = 16.0 / V, c1 = 2.91
-
-a2 = 1e-3 * [Mg2+] * exp( -c2 * V - c3) mM^{-1} s, c2 = 45.0 / V, c3 = 6.97
-
-b1 = 1e3 * exp(c4 * V + c5) s^{-1}, c4 = 9.0 / V, c5 = 1.22
-
-b2 = 1e3 * exp(c6 * V + c7) s^{-1}, c6 = 17.0 / V, c7 = 0.96
-
-A = 1e3 * exp(-c8) s^{-1}, c8 = 2.847
-
-B1 = 1e3 * exp(-c9) s^{-1}, c9 = 0.693 s^{-1}
-
-B2 = 1e3 * exp(-c10) s^{-1}, c10 = 3.101.
-
-The behaviour of S(t) is as follows:
-
-If a spike arrives, then the slope of the linear rise of S(t) is incremented by weight / tau2.
-
-After tau2 time, this component is removed from the slope (reduced by weight/tau) and added over to the rate of decay of S(t).
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`numSynapses`** `unsigned int` Number of synapses on SynBase
-**`Gbar`** `double` Maximal channel conductance
-**`Ek`** `double` Reversal potential of channel
-**`Gk`** `double` Channel conductance variable
-**`Ik`** `double` Channel current variable
-**`tau1`** `double` Decay time constant for the synaptic conductance, tau1 >= tau2.
-**`tau2`** `double` Rise time constant for the synaptic conductance, tau1 >= tau2.
-**`normalizeWeights`** `bool` Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.
-**`unblocked`** `double` Fraction of channels recovered from Mg2+ block. This is an intermediate variable which corresponds to g(V, [Mg2+]o) in the equation for conductance: k * g(V, [Mg2+]o) * S(t) where k is a constant.
-**`MgConc`** `double` External Mg2+ concentration
-**`unblocked`** `double` Fraction of channels recovered from Mg2+ block. This is an intermediate variable which corresponds to g(V, [Mg2+]o) in the equation for conductance: k * g(V, [Mg2+]o) * S(t) where k is a constant.
-**`saturation`** `double` Upper limit on the NMDA conductance.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`permeability`** `double` Conductance term going out to GHK object
-**`IkOut`** `double` Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`activation`** `double` Sometimes we want to continuously activate the channel
-**`modulator`** `double` Modulate channel response
-**`MgConcDest`** `double` Update [Mg2+] from other sources at every time step.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message to Goldman-Hodgkin-Katz object
-**`proc`** `void` Shared message to receive Process message from scheduler
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`c`** `unsigned int,double` Transition parameters c0 to c10 in the Mg2+ dependentstate transitions.
-
-
-## Nernst
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`E`** `double` Computed reversal potential
-**`Temperature`** `double` Temperature of cell
-**`valence`** `int` Valence of ion in Nernst calculation
-**`Cin`** `double` Internal conc of ion
-**`Cout`** `double` External conc of ion
-**`scale`** `double` Voltage scale factor
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`Eout`** `double` Computed reversal potential
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`ci`** `double` Set internal conc of ion, and immediately send out the updated E
-**`co`** `double` Set external conc of ion, and immediately send out the updated E
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## NeuroMesh
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`size`** `double` Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.
-**`numDimensions`** `unsigned int` Number of spatial dimensions of this compartment. Usually 3 or 2
-**`cell`** `Id` Id for base element of cell model. Uses this to traverse theentire tree of the cell to build the mesh.
-**`subTree`** `vector<Id>` Set of compartments to model. If they happen to be contiguousthen also set up diffusion between the compartments. Can alsohandle cases where the same cell is divided into multiplenon-diffusively-coupled compartments
-**`skipSpines`** `bool` Flag: when skipSpines is true, the traversal does not includeany compartment with the string 'spine' or 'neck' in its name,and also then skips compartments below this skipped one.Allows to set up separate mesh for spines, based on the same cell model.
-**`numSegments`** `unsigned int` Number of cylindrical/spherical segments in model
-**`numDiffCompts`** `unsigned int` Number of diffusive compartments in model
-**`diffLength`** `double` Diffusive length constant to use for subdivisions. The system willattempt to subdivide cell using diffusive compartments ofthe specified diffusion lengths as a maximum.In order to get integral numbersof compartments in each segment, it may subdivide more finely.Uses default of 0.5 microns, that is, half typical lambda.For default, consider a tau of about 1 second for mostreactions, and a diffusion const of about 1e-12 um^2/sec.This gives lambda of 1 micron
-**`geometryPolicy`** `string` Policy for how to interpret electrical model geometry (which is a branching 1-dimensional tree) in terms of 3-D constructslike spheres, cylinders, and cones.There are three options, default, trousers, and cylinder:default mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites and dendrites emerging from soma, proximal diameter is from compt dia. Don't worry about overlap. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.trousers mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites, use a trouser function. Avoid overlap. - For soma, use some variant of trousers. Here we must avoid overlap - For spines, use a way to smoothly merge into parent dend. Radius of curvature should be similar to that of the spine neck. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.cylinder mode: - Use cylinders. Diameter is just compartment dia. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle. - Ignore spatial overlap.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`meshSplit`** `double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >` Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.
-**`meshStats`** `unsigned int,vector<double>` Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`buildDefaultMesh`** `double,unsigned int` Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.
-**`handleRequestMeshStats`** `void` Handles request from SimManager for mesh stats
-**`handleNodeInfo`** `unsigned int,unsigned int` Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.
-**`setCellPortion`** `Id,vector<Id>` Tells NeuroMesh to mesh up a subpart of a cell. For nowassumed contiguous.The first argument is the cell Id. The second is the vectorof Ids to consider in meshing up the subpart.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`nodeMeshing`** `void` Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Neuron
-**Author**: C H Chaitanya
-
-**Description**: Neuron - A compartment container
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Neutral
-**Author**: Upinder S. Bhalla, 2007, NCBS
-
-**Description**: Neutral: Base class for all MOOSE classes. Providesaccess functions for housekeeping fields and operations, messagetraversal, and so on.
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## OneToAllMsg
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`e1`** `Id` Id of source Element.
-**`e2`** `Id` Id of source Element.
-**`srcFieldsOnE1`** `vector<string>` Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector
-**`destFieldsOnE2`** `vector<string>` Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector
-**`srcFieldsOnE2`** `vector<string>` Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector
-**`destFieldsOnE1`** `vector<string>` Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
-**`i1`** `DataId` DataId of source Element.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## OneToOneMsg
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`e1`** `Id` Id of source Element.
-**`e2`** `Id` Id of source Element.
-**`srcFieldsOnE1`** `vector<string>` Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector
-**`destFieldsOnE2`** `vector<string>` Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector
-**`srcFieldsOnE2`** `vector<string>` Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector
-**`destFieldsOnE1`** `vector<string>` Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## PIDController
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`gain`** `double` This is the proportional gain (Kp). This tuning parameter scales the proportional term. Larger gain usually results in faster response, but too much will lead to instability and oscillation.
-**`saturation`** `double` Bound on the permissible range of output. Defaults to maximum double value.
-**`command`** `double` The command (desired) value of the sensed parameter. In control theory this is commonly known as setpoint(SP).
-**`sensed`** `double` Sensed (measured) value. This is commonly known as process variable(PV) in control theory.
-**`tauI`** `double` The integration time constant, typically = dt. This is actually proportional gain divided by integral gain (Kp/Ki)). Larger Ki (smaller tauI) usually leads to fast elimination of steady state errors at the cost of larger overshoot.
-**`tauD`** `double` The differentiation time constant, typically = dt / 4. This is derivative gain (Kd) times proportional gain (Kp). Larger Kd (tauD) decreases overshoot at the cost of slowing down transient response and may lead to instability.
-**`output`** `double` Output of the PIDController. This is given by: gain * ( error + INTEGRAL[ error dt ] / tau_i + tau_d * d(error)/dt )
- Where gain = proportional gain (Kp), tau_i = integral gain (Kp/Ki) and tau_d = derivative gain (Kd/Kp). In control theory this is also known as the manipulated variable (MV)
-**`error`** `double` The error term, which is the difference between command and sensed value.
-**`integral`** `double` The integral term. It is calculated as INTEGRAL(error dt) = previous_integral + dt * (error + e_previous)/2.
-**`derivative`** `double` The derivative term. This is (error - e_previous)/dt.
-**`e_previous`** `double` The error term for previous step.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`outputOut`** `double` Sends the output of the PIDController. This is known as manipulated variable (MV) in control theory. This should be fed into the process which we are trying to control.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`commandIn`** `double` Command (desired value) input. This is known as setpoint (SP) in control theory.
-**`sensedIn`** `double` Sensed parameter - this is the one to be tuned. This is known as process variable (PV) in control theory. This comes from the process we are trying to control.
-**`gainDest`** `double` Destination message to control the PIDController gain dynamically.
-**`process`** `void` Handle process calls.
-**`reinit`** `void` Reinitialize the object.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Panel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`nPts`** `unsigned int` Number of points used by panel to specify geometry
-**`nDims`** `unsigned int` Number of Dimensions used by panel to specify geometry
-**`numNeighbors`** `unsigned int` Number of Neighbors of panel
-**`shapeId`** `unsigned int` Identifier for shape type, as used by Smoldyn
-**`coords`** `vector<double>` All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toNeighbor`** `void` Identifies neighbors of the current panel
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`neighbor`** `void` Handles incoming message from neighbor
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`x`** `unsigned int,double` x coordinate identified by index
-**`y`** `unsigned int,double` y coordinate identified by index
-**`z`** `unsigned int,double` z coordinate identified by index
-
-
-## Pool
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-**`increment`** `double` Increments mol numbers by specified amount. Can be +ve or -ve
-**`decrement`** `double` Decrements mol numbers by specified amount. Can be +ve or -ve
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## PoolBase
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Port
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`scaleOutRate`** `double` Scaling factor for outgoing rates. Applies to the RateTermscontrolled by this port. Represents a diffusion related term,or the permeability of the port
-**`inStart`** `unsigned int` Start index to S_ vector into which incoming molecules should add.
-**`inEnd`** `unsigned int` End index to S_ vector into which incoming molecules should add.
-**`outStart`** `unsigned int` Start index to S_ vector from where outgoing molecules come.
-**`outEnd`** `unsigned int` End index to S_ vector from where outgoing molecules come.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`availableMolsAtPort`** `vector<Id>` Sends out the full set of molecule Ids that are available for data transfer
-**`efflux`** `vector<double>` Molecule #s going out
-**`matchedMolsAtPort`** `vector<Id>` Sends out the set of molecule Ids that match between both ports
-**`efflux`** `vector<double>` Molecule #s going out
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`handleMatchedMolsAtPort`** `vector<unsigned int>` Handles list of matched molecules worked out by the other port
-**`influx`** `vector<double>` Molecule #s coming back in
-**`handleAvailableMolsAtPort`** `vector<unsigned int>` Handles list of all species that the other port cares about
-**`influx`** `vector<double>` Molecule #s coming back in
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`port1`** `void` Shared message for port. This one initiates the request forsetting up the communications between the portsThe shared message also handles the runtime data transfer
-**`port2`** `void` Shared message for port. This one responds to the request forsetting up the communications between the portsThe shared message also handles the runtime data transfer
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## PulseGen
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`output`** `double` Output amplitude
-**`baseLevel`** `double` Basal level of the stimulus
-**`firstLevel`** `double` Amplitude of the first pulse in a sequence
-**`firstWidth`** `double` Width of the first pulse in a sequence
-**`firstDelay`** `double` Delay to start of the first pulse in a sequence
-**`secondLevel`** `double` Amplitude of the second pulse in a sequence
-**`secondWidth`** `double` Width of the second pulse in a sequence
-**`secondDelay`** `double` Delay to start of of the second pulse in a sequence
-**`count`** `unsigned int` Number of pulses in a sequence
-**`trigMode`** `unsigned int` Trigger mode for pulses in the sequence.
- 0 : free-running mode where it keeps looping its output
- 1 : external trigger, where it is triggered by an external input (and stops after creating the first train of pulses)
- 2 : external gate mode, where it keeps generating the pulses in a loop as long as the input is high.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`outputOut`** `double` Current output level.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`input`** `double` Handle incoming input that determines gating/triggering onset.
-**`levelIn`** `unsigned int,double` Handle level value coming from other objects
-**`widthIn`** `unsigned int,double` Handle width value coming from other objects
-**`delayIn`** `unsigned int,double` Handle delay value coming from other objects
-**`process`** `void` Handles process call, updates internal time stamp.
-**`reinit`** `void` Handles reinit call.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`level`** `unsigned int,double` Level of the pulse at specified index
-**`width`** `unsigned int,double` Width of the pulse at specified index
-**`delay`** `unsigned int,double` Delay of the pulse at specified index
-
-
-## RC
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`V0`** `double` Initial value of 'state'
-**`R`** `double` Series resistance of the RC circuit.
-**`C`** `double` Parallel capacitance of the RC circuit.
-**`state`** `double` Output value of the RC circuit. This is the voltage across the capacitor.
-**`inject`** `double` Input value to the RC circuit.This is handled as an input current to the circuit.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`outputOut`** `double` Current output level.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`injectIn`** `double` Receives input to the RC circuit. All incoming messages are summed up to give the total input current.
-**`process`** `void` Handles process call.
-**`reinit`** `void` Handle reinitialization
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Reac
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`kf`** `double` Forward rate constant, in # units
-**`kb`** `double` Reverse rate constant, in # units
-**`Kf`** `double` Forward rate constant, in concentration units
-**`Kb`** `double` Reverse rate constant, in concentration units
-**`numSubstrates`** `unsigned int` Number of substrates of reaction
-**`numProducts`** `unsigned int` Number of products of reaction
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the reac to recompute its numRates, as remeshing has happened
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate pool
-**`prd`** `void` Connects to substrate pool
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ReacBase
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`kf`** `double` Forward rate constant, in # units
-**`kb`** `double` Reverse rate constant, in # units
-**`Kf`** `double` Forward rate constant, in concentration units
-**`Kb`** `double` Reverse rate constant, in concentration units
-**`numSubstrates`** `unsigned int` Number of substrates of reaction
-**`numProducts`** `unsigned int` Number of products of reaction
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the reac to recompute its numRates, as remeshing has happened
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate pool
-**`prd`** `void` Connects to substrate pool
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## RectPanel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`nPts`** `unsigned int` Number of points used by panel to specify geometry
-**`nDims`** `unsigned int` Number of Dimensions used by panel to specify geometry
-**`numNeighbors`** `unsigned int` Number of Neighbors of panel
-**`shapeId`** `unsigned int` Identifier for shape type, as used by Smoldyn
-**`coords`** `vector<double>` All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toNeighbor`** `void` Identifies neighbors of the current panel
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`neighbor`** `void` Handles incoming message from neighbor
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`x`** `unsigned int,double` x coordinate identified by index
-**`y`** `unsigned int,double` y coordinate identified by index
-**`z`** `unsigned int,double` z coordinate identified by index
-
-
-## ReduceMsg
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`e1`** `Id` Id of source Element.
-**`e2`** `Id` Id of source Element.
-**`srcFieldsOnE1`** `vector<string>` Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector
-**`destFieldsOnE2`** `vector<string>` Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector
-**`srcFieldsOnE2`** `vector<string>` Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector
-**`destFieldsOnE1`** `vector<string>` Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
-**`i1`** `DataId` DataId of source Element.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Shell
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`reduceArraySize`** `unsigned int` Look up maximum value of an index, here ragged array size,across many nodes, and assign uniformly to all nodes. Normallyfollowed by an operation to assign the size to the object thatwas resized.
-**`requestCreate`** `string,Id,Id,string,vector<int>` requestCreate( class, parent, newElm, name, dimensions ): creates a new Element on all nodes with the specified Id. Initiates a callback to indicate completion of operation. Goes to all nodes including self.
-**`requestDelete`** `Id` requestDelete( doomedElement ):Deletes specified Element on all nodes.Initiates a callback to indicate completion of operation.Goes to all nodes including self.
-**`requestAddMsg`** `string,unsigned int,ObjId,string,ObjId,string` requestAddMsg( type, src, srcField, dest, destField );Creates specified Msg between specified Element on all nodes.Initiates a callback to indicate completion of operation.Goes to all nodes including self.
-**`requestQuit`** `void` requestQuit():Emerges from the inner loop, and wraps up. No return value.
-**`move`** `Id,Id` move( origId, newParent);Moves origId to become a child of newParent
-**`copy`** `vector<Id>,string,unsigned int,bool,bool` copy( origId, newParent, numRepeats, toGlobal, copyExtMsg );Copies origId to become a child of newParent
-**`useClock`** `string,string,unsigned int` useClock( path, field, tick# );Specifies which clock tick to use for all elements in Path.The 'field' is typically process, but some cases need to sendupdates to the 'init' field.Tick # specifies which tick to be attached to the objects.
-**`sync`** `Id,unsigned int` sync( ElementId, FuncId );Synchronizes Element data indexing across all nodes.Used when distributed ops like message setup might set updifferent #s of data entries on Elements on different nodes.The ElementId is the element being synchronized.The FuncId is the 'get' function for the synchronized field.
-**`requestReMesh`** `Id` requestReMesh( meshId );Chops up specified mesh.
-**`requestSetParserIdleFlag`** `bool` SetParserIdleFlag( bool isParserIdle );When True, the main ProcessLoop waits a little each cycleso as to avoid pounding on the CPU.
-**`ack`** `unsigned int,unsigned int` ack( unsigned int node#, unsigned int status ):Acknowledges receipt and completion of a command on a worker node.Goes back only to master node.
-**`requestStart`** `double` requestStart( runtime ):Starts a simulation. Goes to all nodes including self.Initiates a callback to indicate completion of run.
-**`requestStep`** `unsigned int` requestStep():Advances a simulation for the specified # of steps.Goes to all nodes including self.
-**`requestStop`** `void` requestStop():Gently stops a simulation after completing current ops.After this op it is save to do 'start' again, and it willresume where it left offGoes to all nodes including self.
-**`requestSetupTick`** `unsigned int,double` requestSetupTick():Asks the Clock to coordinate the assignment of a specificclock tick. Args: Tick#, dt.Goes to all nodes including self.
-**`requestReinit`** `void` requestReinit():Reinits a simulation: sets to time 0.If simulation is running it stops it first.Goes to all nodes including self.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`receiveGet`** `bad` receiveGet( Uint node#, Uint status, PrepackedBuffer data )Function on master shell that handles the value relayed from worker.
-**`setclock`** `unsigned int,double,bool` Assigns clock ticks. Args: tick#, dt
-**`handleAck`** `unsigned int,unsigned int` Keeps track of # of acks to a blocking shell command. Arg: Source node num.
-**`create`** `string,Id,Id,string,vector<int>` create( class, parent, newElm, name, dimensions )
-**`delete`** `Id` Destroys Element, all its messages, and all its children. Args: Id
-**`handleAddMsg`** `string,unsigned int,ObjId,string,ObjId,string` Makes a msg
-**`handleQuit`** `void` Stops simulation running and quits the simulator
-**`move`** `Id,Id` handleMove( Id orig, Id newParent ): moves an Element to a new parent
-**`handleCopy`** `vector<Id>,string,unsigned int,bool,bool` handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): The vector< Id > has Id orig, Id newParent, Id newElm. This function copies an Element and all its children to a new parent. May also expand out the original into nCopies copies. Normally all messages within the copy tree are also copied. If the flag copyExtMsgs is true, then all msgs going out are also copied.
-**`handleUseClock`** `string,string,unsigned int` Deals with assignment of path to a given clock.
-**`handleSync`** `Id,unsigned int` handleSync( Id Element): Synchronizes DataHandler indexing across nodesThe ElementId is the element being synchronized.The FuncId is the 'get' function for the synchronized field.
-**`handleReMesh`** `Id` handleReMesh( Id BaseMesh): Deals with outcome of resizing the meshing in a cellularcompartment (the ChemMesh class). The mesh change has topropagate down to the molecules and reactions managed by this.Mesh. The ElementId is the mesh being synchronized.
-**`handleSetParserIdleFlag`** `bool` handleSetParserIdleFlag( bool isParserIdle ): When True, tells the ProcessLoop to wait as the Parser is idle.
-**`handleAck`** `unsigned int,unsigned int` Keeps track of # of acks to a blocking shell command. Arg: Source node num.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`master`** `void` Issues commands from master shell to worker shells located on different nodes. Also handles acknowledgements from them.
-**`worker`** `void` Handles commands arriving from master shell on node 0.Sends out acknowledgements from them.
-**`clockControl`** `void` Controls the system Clock
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SimManager
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`syncTime`** `double` SyncTime is the interval between synchronizing solvers5 msec is a typical value
-**`autoPlot`** `bool` When the autoPlot flag is true, the simManager guesses whichplots are of interest, and builds them.
-**`plotDt`** `double` plotDt is the timestep for plotting variables. As most will bechemical, a default of 1 sec is reasonable
-**`runTime`** `double` runTime is the requested duration of the simulation that is stored in some kinds of model definition files.
-**`method`** `string` method is the numerical method used for the calculations.This will set up or even replace the solver with one ableto use the specified method. Currently works only with two solvers: GSL and GSSA.The GSL solver has a variety of ODE methods, by defaultRunge-Kutta-Fehlberg.The GSSA solver currently uses the Gillespie StochasticSystems Algorithm, somewhat optimized over the originalmethod.
-**`version`** `unsigned int` Numerical version number. Used by kkit
-**`modelFamily`** `string` Family classification of model: *kinetic, and *neuron are the options so far. In due course expect to see thingslike detailedNetwork, intFireNetwork, sigNeur and so on.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`requestMeshStats`** `void` Asks for basic stats for mesh:Total # of entries, and a vector of unique volumes of voxels
-**`nodeInfo`** `unsigned int,unsigned int` Sends out # of nodes to use for meshing, and # of threads to use on each node, to the ChemMesh. These numbers sometimesdiffer from the total # of nodes and threads, because the SimManager may have other portions of the model to allocate.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`build`** `string` Sets up model, with the specified method. The method may beempty if the intention is that methods be set up through hints in the ChemMesh compartments.
-**`makeStandardElements`** `string` Sets up the usual infrastructure for a model, with theChemMesh, Stoich, solver and suitable messaging.The argument is the MeshClass to use.
-**`meshSplit`** `double,vector<unsigned int>,vector<unsigned int>,vector<unsigned int>,vector<unsigned int>` Handles message from ChemMesh that defines howmeshEntries communicate between nodes.First arg is oldvol, next is list of other nodes, third arg is list number ofmeshEntries to be transferred for each of these nodes, fourth arg is catenated list of meshEntries indices onmy node going to each of the other connected nodes, andlast arg is matching list of meshEntries on other nodes
-**`meshStats`** `unsigned int,vector<double>` Basic statistics for mesh: Total # of entries, and a vectorof unique volumes of voxels
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`nodeMeshing`** `void` Connects to ChemMesh to coordinate meshing with paralleldecomposition and with the Stoich
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SingleMsg
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`e1`** `Id` Id of source Element.
-**`e2`** `Id` Id of source Element.
-**`srcFieldsOnE1`** `vector<string>` Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector
-**`destFieldsOnE2`** `vector<string>` Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector
-**`srcFieldsOnE2`** `vector<string>` Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector
-**`destFieldsOnE1`** `vector<string>` Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
-**`i1`** `DataId` Index of source object.
-**`i2`** `DataId` Index of dest object.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SolverJunction
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`numReacs`** `unsigned int` Number of cross-compartment reactions on this Junction
-**`numDiffMols`** `unsigned int` Number of molecule species diffusing across this Junction
-**`numMeshEntries`** `unsigned int` Number of voxels (mesh entries) handled by Junction
-**`otherCompartment`** `Id` Id of compartment on other side of this Junction. Readily obtained by message traversal, just a utility field.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`junctionPoolNum`** `vector<double>` Sends out vector of all mol #s needed to compute junction rates.
-**`junctionPoolDelta`** `vector<double>` Sends out vector of all mol # changes going across junction.
-**`junctionPoolNum`** `vector<double>` Sends out vector of all mol #s needed to compute junction rates.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`handleJunctionPoolNum`** `vector<double>` Handles vector of doubles specifying pool num, that arrive at the Junction, by redirecting up to parent StoichPools object
-**`handleJunctionPoolNum`** `vector<double>` Handles vector of doubles specifying pool num, that arrive at the Junction, by redirecting up to parent StoichPools object
-**`handleJunctionPoolDelta`** `vector<double>` Handles vector of doubles with pool num changes that arrive at the Junction, by redirecting up to parent StoichPools object
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`symJunction`** `void` Symmetric shared message between SolverJunctions to handle cross-solver reactions and diffusion. This variant sends only pool mol#s, and is symmetric.
-**`masterJunction`** `void` Shared message between SolverJunctions to handle cross-solver reactions and diffusion. This sends the change in pool #, of abutting voxels, and receives the pool# of the same abutting voxels. Thus it operates on the solver that is doing the diffusion calculations. This will typically be the solver that operates at a finer level of detail. The order of detail is Smoldyn > Gillespie > deterministic. For two identical solvers we would typically have one with the finer grid size become the master Junction.
-**`followerJunction`** `void` Shared message between SolverJunctions to handle cross-solver reactions and diffusion. This sends the pool #, of its boundary voxels, and receives back changes in the pool# of the same boundary voxels voxels. Thus it operates on the solver that is just tracking the diffusion calculations that the other (master) solver is doing
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SparseMsg
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`e1`** `Id` Id of source Element.
-**`e2`** `Id` Id of source Element.
-**`srcFieldsOnE1`** `vector<string>` Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector
-**`destFieldsOnE2`** `vector<string>` Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector
-**`srcFieldsOnE2`** `vector<string>` Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector
-**`destFieldsOnE1`** `vector<string>` Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
-**`numRows`** `unsigned int` Number of rows in matrix.
-**`numColumns`** `unsigned int` Number of columns in matrix.
-**`numEntries`** `unsigned int` Number of Entries in matrix.
-**`probability`** `double` connection probability for random connectivity.
-**`seed`** `long` Random number seed for generating probabilistic connectivity.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`setRandomConnectivity`** `double,long` Assigns connectivity with specified probability and seed
-**`setEntry`** `unsigned int,unsigned int,unsigned int` Assigns single row,column value
-**`unsetEntry`** `unsigned int,unsigned int` Clears single row,column entry
-**`clear`** `void` Clears out the entire matrix
-**`transpose`** `void` Transposes the sparse matrix
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Species
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`molWt`** `double` Molecular weight of species
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`sendMolWt`** `double` returns molWt.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`handleMolWtRequest`** `void` Handle requests for molWt.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`pool`** `void` Connects to pools of this Species type
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SpherePanel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`nPts`** `unsigned int` Number of points used by panel to specify geometry
-**`nDims`** `unsigned int` Number of Dimensions used by panel to specify geometry
-**`numNeighbors`** `unsigned int` Number of Neighbors of panel
-**`shapeId`** `unsigned int` Identifier for shape type, as used by Smoldyn
-**`coords`** `vector<double>` All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toNeighbor`** `void` Identifies neighbors of the current panel
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`neighbor`** `void` Handles incoming message from neighbor
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`x`** `unsigned int,double` x coordinate identified by index
-**`y`** `unsigned int,double` y coordinate identified by index
-**`z`** `unsigned int,double` z coordinate identified by index
-
-
-## SpikeGen
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`threshold`** `double` Spiking threshold, must cross it going up
-**`refractT`** `double` Refractory Time.
-**`abs_refract`** `double` Absolute refractory time. Synonym for refractT.
-**`hasFired`** `bool` True if SpikeGen has just fired
-**`edgeTriggered`** `bool` When edgeTriggered = 0, the SpikeGen will fire an event in each timestep while incoming Vm is > threshold and at least abs_refracttime has passed since last event. This may be problematic if the incoming Vm remains above threshold for longer than abs_refract. Setting edgeTriggered to 1 resolves this as the SpikeGen generatesan event only on the rising edge of the incoming Vm and will remain idle unless the incoming Vm goes below threshold.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`event`** `double` Sends out a trigger for an event.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`Vm`** `double` Handles Vm message coming in from compartment
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message to receive Process message from scheduler
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Stats
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`mean`** `double` Mean of all sampled values.
-**`sdev`** `double` Standard Deviation of all sampled values.
-**`sum`** `double` Sum of all sampled values.
-**`num`** `unsigned int` Number of all sampled values.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`reduce`** `unsigned int` Execute statistics reduction operation on all targets andplace results in this object
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`trig`** `void` Triggers Reduction operation.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## StimulusTable
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`vec`** `vector<double>` vector with all table entries
-**`outputValue`** `double` Output value holding current table entry or output of a calculation
-**`size`** `unsigned int` size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest
-**`startTime`** `double` Start time used when table is emitting values. For lookupvalues below this, the table just sends out its zero entry.Corresponds to zeroth entry of table.
-**`stopTime`** `double` Time to stop emitting values.If time exceeds this, then the table sends out its last entry.The stopTime corresponds to the last entry of table.
-**`loopTime`** `double` If looping, this is the time between successive cycle starts.Defaults to the difference between stopTime and startTime, so that the output waveform cycles with precisely the same duration as the table contents.If larger than stopTime - startTime, then it pauses at the last table value till it is time to go around again.If smaller than stopTime - startTime, then it begins the next cycle even before the first one has reached the end of the table.
-**`stepSize`** `double` Increment in lookup (x) value on every timestep. If it isless than or equal to zero, the StimulusTable uses the current timeas the lookup value.
-**`stepPosition`** `double` Current value of lookup (x) value.If stepSize is less than or equal to zero, this is set tothe current time to use as the lookup value.
-**`doLoop`** `bool` Flag: Should it loop around to startTime once it has reachedstopTime. Default (zero) is to do a single pass.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`output`** `double` Sends out tabulated data according to lookup parameters.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`linearTransform`** `double,double` Linearly scales and offsets data. Scale first, then offset.
-**`xplot`** `string,string` Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname
-**`plainPlot`** `string` Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename
-**`loadCSV`** `string,int,int,char` Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator
-**`loadXplot`** `string,string` Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.
-**`loadXplotRange`** `string,string,unsigned int,unsigned int` Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.
-**`compareXplot`** `string,string,string` Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
-**`compareVec`** `vector<double>,string` Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
-**`clearVec`** `void` Handles request to clear the data vector
-**`process`** `void` Handles process call, updates internal time stamp.
-**`reinit`** `void` Handles reinit call.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`y`** `unsigned int,double` Value of table at specified index
-
-
-## Stoich
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`useOneWayReacs`** `bool` Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations
-**`nVarPools`** `unsigned int` Number of variable molecule pools in the reac system
-**`numMeshEntries`** `unsigned int` Number of meshEntries in reac-diff system
-**`estimatedDt`** `double` Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.
-**`path`** `string` Path of reaction system to take over
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`plugin`** `Id` Sends out Stoich Id so that plugins can directly access fields and functions
-**`nodeDiffBoundary`** `unsigned int,vector<unsigned int>,vector<double>` Sends mol #s across boundary between nodes, to calculate diffusionterms. arg1 is originating node, arg2 is list of meshIndices forwhich data is being transferred, and arg3 are the 'n' values forall the pools on the specified meshIndices, to be plugged intothe appropriate place on the recipient node's S_ matrix
-**`poolsReactingAcrossBoundary`** `unsigned int,vector<double>` A vector of mol counts (n) of those pools that react across a boundary. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.
-**`reacRollbacksAcrossBoundary`** `unsigned int,vector<double>` Occasionally, a Gillespie advance will cause the mol conc on the target stoich side to become negative. If so, this message does a patch up job by telling the originating Stoich to roll back to the specified number of reac firings, which is the max that the target was able to handle. This is probably numerically naughty, but it is better than negative concentrations
-**`reacRatesAcrossBoundary`** `unsigned int,vector<double>` A vector of reac rates (V) of each reaction crossing the boundary between compartments. Sent over to another Stoich every sync timestep so that the target Stoich has both sides of the boundary reaction. In the case of Gillespie calculations *V* is the integer # of transitions (firings) of each reaction. Assumes that the mesh encolosing the target Stoich also encloses the reaction object.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`meshSplit`** `double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >` Handles message from ChemMesh that defines how meshEntries are decomposed on this node, and how they communicate between nodes.Args: (oldVol, volumeVectorForAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#])
-**`handleReacRatesAcrossBoundary`** `unsigned int,vector<double>` When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.
-**`handlePoolsReactingAcrossBoundary`** `unsigned int,vector<double>` When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of pool #s for every pool that reacts across the boundary, in every mesh entry. that reacts across a boundary, in every mesh entry
-**`handleReacRollbacksAcrossBoundary`** `unsigned int,vector<double>` When we have reactions that cross compartment boundaries, we may have different solvers and meshes on either side. Only one side does the calculations to assure mass conservation. There are rare cases when the calculations of one solver, typically a Gillespie one, gives such a large change that the concentrations on the other side would become negative in one or more molecules This message handles such cases on the Gillespie side, by telling the solver to roll back its recent calculation and instead use the specified vector for the rates, that is the # of mols changed in the latest timestep. This message handle info for two things: Arg 1: An identifier for the boundary. Arg 2: A vector of reaction rates for every reaction across the boundary, in every mesh entry.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`boundaryReacOut`** `void` Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.
-**`boundaryReacIn`** `void` Shared message between Stoichs to handle reactions taking molecules between the pools handled by the two Stoichs.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## StoichCore
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`useOneWayReacs`** `bool` Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations
-**`nVarPools`** `unsigned int` Number of variable molecule pools in the reac system
-**`estimatedDt`** `double` Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.
-**`path`** `string` Path of reaction system to take over
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## StoichPools
-**Author**: Upinder S. Bhalla, 2012, NCBS
-
-**Description**: Pure virtual base class for handling reaction pools. GslStoich is derived from this.
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`addJunction`** `Id` Add a junction between the current solver and the one whose Id is passed in.
-**`dropJunction`** `Id` Drops a junction between the current solver and the one whose Id is passed in. Ignores if no junction.
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SumFunc
-**Author**: Upi Bhalla
-
-**Description**: SumFunc object. Adds up all inputs
-
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`result`** `double` Outcome of function computation
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`output`** `double` Sends out sum on each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`input`** `double` Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Surface
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`volume`** `double` This is something I'll need to write a function to compute.Perhaps have an update routine as it may be hard to compute but is needed often by the molecules.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`absorb`** `void` these help the system define non-standard operations for what a molecule does when it hits a surface.The default is reflect.As a molecule may interact with multiple surfaces, it isn't enough to confer a property on the molecule itself. We have to use messages. Perhaps we don't need these, but instead put entities on the surface which the molecule interacts with if it doesn't do the basic reflect operation.
-**`transmit`** `void` Surface lets molecules through
-**`jump`** `void` dunno
-**`mixture`** `void` dunno
-**`surface`** `double,double,double` Connects up to a compartment, either as interior or exterior Args are volume, area, perimeter
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SymCompartment
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Vm`** `double` membrane potential
-**`Cm`** `double` Membrane capacitance
-**`Em`** `double` Resting membrane potential
-**`Im`** `double` Current going through membrane
-**`inject`** `double` Current injection to deliver into compartment
-**`initVm`** `double` Initial value for membrane potential
-**`Rm`** `double` Membrane resistance
-**`Ra`** `double` Axial resistance of compartment
-**`diameter`** `double` Diameter of compartment
-**`length`** `double` Length of compartment
-**`x0`** `double` X coordinate of start of compartment
-**`y0`** `double` Y coordinate of start of compartment
-**`z0`** `double` Z coordinate of start of compartment
-**`x`** `double` x coordinate of end of compartment
-**`y`** `double` y coordinate of end of compartment
-**`z`** `double` z coordinate of end of compartment
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`VmOut`** `double` Sends out Vm value of compartment on each timestep
-**`axialOut`** `double` Sends out Vm value of compartment to adjacent compartments,on each timestep
-**`raxialOut`** `double,double` Sends out Raxial information on each timestep, fields are Ra and Vm
-**`raxialOut`** `double,double` Sends out Ra and Vm on each timestep
-**`sumRaxialOut`** `double` Sends out Ra
-**`requestSumAxial`** `void` Sends out request for Ra.
-**`raxialOut`** `double,double` Sends out Ra and Vm on each timestep
-**`sumRaxialOut`** `double` Sends out Ra
-**`requestSumAxial`** `void` Sends out request for Ra.
-**`Raxial2Out`** `double,double` Sends out Ra and Vm
-**`sumRaxial2Out`** `double` Sends out Ra
-**`requestSumAxial2`** `void` Sends out request for Ra.
-**`Raxial2Out`** `double,double` Sends out Ra and Vm
-**`sumRaxial2Out`** `double` Sends out Ra
-**`requestSumAxial2`** `void` Sends out request for Ra.
-**`Raxial2Out`** `double,double` Sends out Ra and Vm
-**`sumRaxial2Out`** `double` Sends out Ra
-**`requestSumAxial2`** `void` Sends out request for Ra.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`injectMsg`** `double` The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
-**`randInject`** `double,double` Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.
-**`injectMsg`** `double` The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
-**`cable`** `void` Message for organizing compartments into groups, calledcables. Doesn't do anything.
-**`process`** `void` Handles 'process' call
-**`reinit`** `void` Handles 'reinit' call
-**`initProc`** `void` Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.
-**`initReinit`** `void` Handles Reinit call for the 'init' phase of the Compartment calculations.
-**`handleChannel`** `double,double` Handles conductance and Reversal potential arguments from Channel
-**`handleRaxial`** `double,double` Handles Raxial info: arguments are Ra and Vm.
-**`handleAxial`** `double` Handles Axial information. Argument is just Vm.
-**`raxialSym`** `double,double` Expects Ra and Vm from other compartment.
-**`sumRaxial`** `double` Expects Ra from other compartment.
-**`handleSumRaxialRequest`** `void` Handle request to send back Ra to originating compartment.
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` This is a shared message to receive Process messages from the scheduler objects. The Process should be called _second_ in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-**`init`** `void` This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.
-**`channel`** `void` This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm
-**`axial`** `void` This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.
-**`raxial`** `void` This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.
-**`raxial1`** `void` This is a raxial shared message between symmetric compartments.It goes from the tail of the current compartment to one closer to the soma.
-**`CONNECTTAIL`** `void` This is a raxial shared message between symmetric compartments.It is an alias for raxial1.
-**`raxial2`** `void` This is a raxial2 shared message between symmetric compartments.It goes from the head of the current compartment to a compartment further away from the soma
-**`CONNECTHEAD`** `void` This is a raxial2 shared message between symmetric compartments.It is an alias for raxial2.It goes from the current compartment to one further from the soma
-**`CONNECTCROSS`** `void` This is a raxial2 shared message between symmetric compartments.It is an alias for raxial2.Conceptually, this goes from the tail of the current compartment to the tail of a sibling compartment. However,this works out to the same as CONNECTHEAD in terms of equivalentcircuit.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SynBase
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`numSynapses`** `unsigned int` Number of synapses on SynBase
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SynChan
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`numSynapses`** `unsigned int` Number of synapses on SynBase
-**`Gbar`** `double` Maximal channel conductance
-**`Ek`** `double` Reversal potential of channel
-**`Gk`** `double` Channel conductance variable
-**`Ik`** `double` Channel current variable
-**`tau1`** `double` Decay time constant for the synaptic conductance, tau1 >= tau2.
-**`tau2`** `double` Rise time constant for the synaptic conductance, tau1 >= tau2.
-**`normalizeWeights`** `bool` Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`permeability`** `double` Conductance term going out to GHK object
-**`IkOut`** `double` Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`activation`** `double` Sometimes we want to continuously activate the channel
-**`modulator`** `double` Modulate channel response
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message to Goldman-Hodgkin-Katz object
-**`proc`** `void` Shared message to receive Process message from scheduler
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## SynChanBase
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`numSynapses`** `unsigned int` Number of synapses on SynBase
-**`Gbar`** `double` Maximal channel conductance
-**`Ek`** `double` Reversal potential of channel
-**`Gk`** `double` Channel conductance variable
-**`Ik`** `double` Channel current variable
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`permeability`** `double` Conductance term going out to GHK object
-**`IkOut`** `double` Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`Vm`** `double` Handles Vm message coming in from compartment
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message to Goldman-Hodgkin-Katz object
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Synapse
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`weight`** `double` Synaptic weight
-**`delay`** `double` Axonal propagation delay to this synapse
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`addSpike`** `double` Handles arriving spike messages, by redirecting up to parent SynBase object
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Table
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`vec`** `vector<double>` vector with all table entries
-**`outputValue`** `double` Output value holding current table entry or output of a calculation
-**`size`** `unsigned int` size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest
-**`threshold`** `double` threshold used when Table acts as a buffer for spikes
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`requestData`** `unsigned int` Sends request for a field to target object
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`linearTransform`** `double,double` Linearly scales and offsets data. Scale first, then offset.
-**`xplot`** `string,string` Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname
-**`plainPlot`** `string` Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename
-**`loadCSV`** `string,int,int,char` Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator
-**`loadXplot`** `string,string` Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.
-**`loadXplotRange`** `string,string,unsigned int,unsigned int` Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.
-**`compareXplot`** `string,string,string` Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
-**`compareVec`** `vector<double>,string` Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
-**`clearVec`** `void` Handles request to clear the data vector
-**`input`** `double` Fills data into the Table.
-**`spike`** `double` Fills spike timings into the Table. Signal has to exceed thresh
-**`recvData`** `bad` Handles data sent back following request
-**`process`** `void` Handles process call, updates internal time stamp.
-**`reinit`** `void` Handles reinit call.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`y`** `unsigned int,double` Value of table at specified index
-
-
-## TableBase
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`vec`** `vector<double>` vector with all table entries
-**`outputValue`** `double` Output value holding current table entry or output of a calculation
-**`size`** `unsigned int` size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`linearTransform`** `double,double` Linearly scales and offsets data. Scale first, then offset.
-**`xplot`** `string,string` Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname
-**`plainPlot`** `string` Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename
-**`loadCSV`** `string,int,int,char` Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator
-**`loadXplot`** `string,string` Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.
-**`loadXplotRange`** `string,string,unsigned int,unsigned int` Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.
-**`compareXplot`** `string,string,string` Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
-**`compareVec`** `vector<double>,string` Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
-**`clearVec`** `void` Handles request to clear the data vector
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`y`** `unsigned int,double` Value of table at specified index
-
-
-## TableEntry
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`value`** `double` Data value in this entry
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## Tick
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`dt`** `double` Timestep for this tick
-**`localdt`** `double` Timestep for this tick
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`process0`** `PK8ProcInfo` Process for Tick 0
-**`reinit0`** `PK8ProcInfo` Reinit for Tick 0
-**`process1`** `PK8ProcInfo` Process for Tick 1
-**`reinit1`** `PK8ProcInfo` Reinit for Tick 1
-**`process2`** `PK8ProcInfo` Process for Tick 2
-**`reinit2`** `PK8ProcInfo` Reinit for Tick 2
-**`process3`** `PK8ProcInfo` Process for Tick 3
-**`reinit3`** `PK8ProcInfo` Reinit for Tick 3
-**`process4`** `PK8ProcInfo` Process for Tick 4
-**`reinit4`** `PK8ProcInfo` Reinit for Tick 4
-**`process5`** `PK8ProcInfo` Process for Tick 5
-**`reinit5`** `PK8ProcInfo` Reinit for Tick 5
-**`process6`** `PK8ProcInfo` Process for Tick 6
-**`reinit6`** `PK8ProcInfo` Reinit for Tick 6
-**`process7`** `PK8ProcInfo` Process for Tick 7
-**`reinit7`** `PK8ProcInfo` Reinit for Tick 7
-**`process8`** `PK8ProcInfo` Process for Tick 8
-**`reinit8`** `PK8ProcInfo` Reinit for Tick 8
-**`process9`** `PK8ProcInfo` Process for Tick 9
-**`reinit9`** `PK8ProcInfo` Reinit for Tick 9
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc0`** `void` Shared proc/reinit message
-**`proc1`** `void` Shared proc/reinit message
-**`proc2`** `void` Shared proc/reinit message
-**`proc3`** `void` Shared proc/reinit message
-**`proc4`** `void` Shared proc/reinit message
-**`proc5`** `void` Shared proc/reinit message
-**`proc6`** `void` Shared proc/reinit message
-**`proc7`** `void` Shared proc/reinit message
-**`proc8`** `void` Shared proc/reinit message
-**`proc9`** `void` Shared proc/reinit message
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## TriPanel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`nPts`** `unsigned int` Number of points used by panel to specify geometry
-**`nDims`** `unsigned int` Number of Dimensions used by panel to specify geometry
-**`numNeighbors`** `unsigned int` Number of Neighbors of panel
-**`shapeId`** `unsigned int` Identifier for shape type, as used by Smoldyn
-**`coords`** `vector<double>` All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toNeighbor`** `void` Identifies neighbors of the current panel
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`neighbor`** `void` Handles incoming message from neighbor
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`x`** `unsigned int,double` x coordinate identified by index
-**`y`** `unsigned int,double` y coordinate identified by index
-**`z`** `unsigned int,double` z coordinate identified by index
-
-
-## VectorTable
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`xdivs`** `unsigned int` Number of divisions.
-**`xmin`** `double` Minimum value in table.
-**`xmax`** `double` Maximum value in table.
-**`invdx`** `double` Maximum value in table.
-**`table`** `vector<double>` The lookup table.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-**`lookupvalue`** `double,double` Lookup function that performs interpolation to return a value.
-**`lookupindex`** `unsigned int,double` Lookup function that returns value by index.
-
-
-## ZBufPool
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZEnz
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Km`** `double` Michaelis-Menten constant in SI conc units (milliMolar)
-**`numKm`** `double` Michaelis-Menten constant in number units, volume dependent
-**`kcat`** `double` Forward rate constant for enzyme, units 1/sec
-**`numSubstrates`** `unsigned int` Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
-**`k1`** `double` Forward reaction from enz + sub to complex
-**`k2`** `double` Reverse reaction from complex to enz + sub
-**`k3`** `double` Forward rate constant from complex to product + enz
-**`ratio`** `double` Ratio of k2/k3
-**`concK1`** `double` K1 expressed in concentration (1/millimolar.sec) units
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-**`toEnz`** `double,double` Sends out increment of molecules on product each timestep
-**`toCplx`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product. Dummy.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the MMEnz to recompute its numKm after remeshing
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`cplxDest`** `double` Handles # of molecules of enz-sub complex
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate molecule
-**`prd`** `void` Connects to product molecule
-**`proc`** `void` Shared message for process and reinit
-**`enz`** `void` Connects to enzyme pool
-**`cplx`** `void` Connects to enz-sub complex pool
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZFuncPool
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-**`input`** `double` Handles input to control value of n_
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZMMenz
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Km`** `double` Michaelis-Menten constant in SI conc units (milliMolar)
-**`numKm`** `double` Michaelis-Menten constant in number units, volume dependent
-**`kcat`** `double` Forward rate constant for enzyme, units 1/sec
-**`numSubstrates`** `unsigned int` Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product. Dummy.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the MMEnz to recompute its numKm after remeshing
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate molecule
-**`prd`** `void` Connects to product molecule
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZPool
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZReac
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`kf`** `double` Forward rate constant, in # units
-**`kb`** `double` Reverse rate constant, in # units
-**`Kf`** `double` Forward rate constant, in concentration units
-**`Kb`** `double` Reverse rate constant, in concentration units
-**`numSubstrates`** `unsigned int` Number of substrates of reaction
-**`numProducts`** `unsigned int` Number of products of reaction
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the reac to recompute its numRates, as remeshing has happened
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate pool
-**`prd`** `void` Connects to substrate pool
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombieBufPool
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombieCaConc
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Ca`** `double` Calcium concentration.
-**`CaBasal`** `double` Basal Calcium concentration.
-**`Ca_base`** `double` Basal Calcium concentration, synonym for CaBasal
-**`tau`** `double` Settling time for Ca concentration
-**`B`** `double` Volume scaling factor
-**`thick`** `double` Thickness of Ca shell.
-**`ceiling`** `double` Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.
-**`floor`** `double` Floor value for Ca concentration. If Ca < floor, Ca = floor
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`concOut`** `double` Concentration of Ca in pool
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`current`** `double` Calcium Ion current, due to be converted to conc.
-**`currentFraction`** `double,double` Fraction of total Ion current, that is carried by Ca2+.
-**`increase`** `double` Any input current that increases the concentration.
-**`decrease`** `double` Any input current that decreases the concentration.
-**`basal`** `double` Synonym for assignment of basal conc.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message to receive Process message from scheduler
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombieCompartment
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Vm`** `double` membrane potential
-**`Cm`** `double` Membrane capacitance
-**`Em`** `double` Resting membrane potential
-**`Im`** `double` Current going through membrane
-**`inject`** `double` Current injection to deliver into compartment
-**`initVm`** `double` Initial value for membrane potential
-**`Rm`** `double` Membrane resistance
-**`Ra`** `double` Axial resistance of compartment
-**`diameter`** `double` Diameter of compartment
-**`length`** `double` Length of compartment
-**`x0`** `double` X coordinate of start of compartment
-**`y0`** `double` Y coordinate of start of compartment
-**`z0`** `double` Z coordinate of start of compartment
-**`x`** `double` x coordinate of end of compartment
-**`y`** `double` y coordinate of end of compartment
-**`z`** `double` z coordinate of end of compartment
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`VmOut`** `double` Sends out Vm value of compartment on each timestep
-**`axialOut`** `double` Sends out Vm value of compartment to adjacent compartments,on each timestep
-**`raxialOut`** `double,double` Sends out Raxial information on each timestep, fields are Ra and Vm
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`injectMsg`** `double` The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
-**`randInject`** `double,double` Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.
-**`injectMsg`** `double` The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
-**`cable`** `void` Message for organizing compartments into groups, calledcables. Doesn't do anything.
-**`process`** `void` Handles 'process' call
-**`reinit`** `void` Handles 'reinit' call
-**`initProc`** `void` Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.
-**`initReinit`** `void` Handles Reinit call for the 'init' phase of the Compartment calculations.
-**`handleChannel`** `double,double` Handles conductance and Reversal potential arguments from Channel
-**`handleRaxial`** `double,double` Handles Raxial info: arguments are Ra and Vm.
-**`handleAxial`** `double` Handles Axial information. Argument is just Vm.
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` This is a shared message to receive Process messages from the scheduler objects. The Process should be called _second_ in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-**`init`** `void` This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.
-**`channel`** `void` This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm
-**`axial`** `void` This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.
-**`raxial`** `void` This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombieEnz
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Km`** `double` Michaelis-Menten constant in SI conc units (milliMolar)
-**`numKm`** `double` Michaelis-Menten constant in number units, volume dependent
-**`kcat`** `double` Forward rate constant for enzyme, units 1/sec
-**`numSubstrates`** `unsigned int` Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
-**`k1`** `double` Forward reaction from enz + sub to complex
-**`k2`** `double` Reverse reaction from complex to enz + sub
-**`k3`** `double` Forward rate constant from complex to product + enz
-**`ratio`** `double` Ratio of k2/k3
-**`concK1`** `double` K1 expressed in concentration (1/millimolar.sec) units
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-**`toEnz`** `double,double` Sends out increment of molecules on product each timestep
-**`toCplx`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product. Dummy.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the MMEnz to recompute its numKm after remeshing
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`cplxDest`** `double` Handles # of molecules of enz-sub complex
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate molecule
-**`prd`** `void` Connects to product molecule
-**`proc`** `void` Shared message for process and reinit
-**`enz`** `void` Connects to enzyme pool
-**`cplx`** `void` Connects to enz-sub complex pool
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombieFuncPool
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-**`input`** `double` Handles input to control value of n_
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombieHHChannel
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Gbar`** `double` Maximal channel conductance
-**`Ek`** `double` Reversal potential of channel
-**`Gk`** `double` Channel conductance variable
-**`Ik`** `double` Channel current variable
-**`Xpower`** `double` Power for X gate
-**`Ypower`** `double` Power for Y gate
-**`Zpower`** `double` Power for Z gate
-**`instant`** `int` Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state
-**`X`** `double` State variable for X gate
-**`Y`** `double` State variable for Y gate
-**`Z`** `double` State variable for Y gate
-**`useConcentration`** `int` Flag: when true, use concentration message rather than Vm tocontrol Z gate
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`channelOut`** `double,double` Sends channel variables Gk and Ek to compartment
-**`permeability`** `double` Conductance term going out to GHK object
-**`IkOut`** `double` Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`Vm`** `double` Handles Vm message coming in from compartment
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`concen`** `double` Incoming message from Concen object to specific conc to usein the Z gate calculations
-**`createGate`** `string` Function to create specified gate.Argument: Gate type [X Y Z]
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`channel`** `void` This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-**`ghk`** `void` Message to Goldman-Hodgkin-Katz object
-**`proc`** `void` This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.
- The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombieMMenz
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`Km`** `double` Michaelis-Menten constant in SI conc units (milliMolar)
-**`numKm`** `double` Michaelis-Menten constant in number units, volume dependent
-**`kcat`** `double` Forward rate constant for enzyme, units 1/sec
-**`numSubstrates`** `unsigned int` Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`enzDest`** `double` Handles # of molecules of Enzyme
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product. Dummy.
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the MMEnz to recompute its numKm after remeshing
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate molecule
-**`prd`** `void` Connects to product molecule
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombiePool
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`n`** `double` Number of molecules in pool
-**`nInit`** `double` Initial value of number of molecules in pool
-**`diffConst`** `double` Diffusion constant of molecule
-**`conc`** `double` Concentration of molecules in this pool
-**`concInit`** `double` Initial value of molecular concentration in pool
-**`size`** `double` Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1
-**`speciesId`** `unsigned int` Species identifier for this mol pool. Eventually link to ontology.
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`nOut`** `double` Sends out # of molecules in pool on each timestep
-**`requestMolWt`** `void` Requests Species object for mol wt
-**`requestSize`** `double` Requests Size of pool from matching mesh entry
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`group`** `void` Handle for grouping. Doesn't do anything.
-**`reacDest`** `double,double` Handles reaction input
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`handleMolWt`** `double` Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-**`remesh`** `double,unsigned int,unsigned int,vector<unsigned int>,vector<double>` Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`reac`** `void` Connects to reaction
-**`proc`** `void` Shared message for process and reinit
-**`species`** `void` Shared message for connecting to species objects
-**`mesh`** `void` Shared message for dealing with mesh operations
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombieReac
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`kf`** `double` Forward rate constant, in # units
-**`kb`** `double` Reverse rate constant, in # units
-**`Kf`** `double` Forward rate constant, in concentration units
-**`Kb`** `double` Reverse rate constant, in concentration units
-**`numSubstrates`** `unsigned int` Number of substrates of reaction
-**`numProducts`** `unsigned int` Number of products of reaction
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`toSub`** `double,double` Sends out increment of molecules on product each timestep
-**`toPrd`** `double,double` Sends out increment of molecules on product each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`subDest`** `double` Handles # of molecules of substrate
-**`prdDest`** `double` Handles # of molecules of product
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-**`remesh`** `void` Tells the reac to recompute its numRates, as remeshing has happened
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`sub`** `void` Connects to substrate pool
-**`prd`** `void` Connects to substrate pool
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## ZombieSumFunc
-
-#### Value fields
-
-Field Type Description
----- ---- ----
-**`this`** `Neutral` Access function for entire object
-**`name`** `string` Name of object
-**`me`** `ObjId` ObjId for current object
-**`parent`** `ObjId` Parent ObjId for current object
-**`children`** `vector<Id>` vector of ObjIds listing all children of current object
-**`path`** `string` text path for object
-**`class`** `string` Class Name of object
-**`linearSize`** `unsigned int` # of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.
-**`objectDimensions`** `vector<unsigned int>` Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.
-**`lastDimension`** `unsigned int` Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.
-**`localNumField`** `unsigned int` For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.
-**`pathIndices`** `vector< vector<unsigned int> >` Indices of the entire path hierarchy leading up to this Object.
-**`msgOut`** `vector<ObjId>` Messages going out from this Element
-**`msgIn`** `vector<ObjId>` Messages coming in to this Element
-**`result`** `double` outcome of summation
-
-
-#### Source message fields
-
-Field Type Description
----- ---- ----
-**`childMsg`** `int` Message to child Elements
-**`output`** `double` Sends out sum on each timestep
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`parentMsg`** `int` Message from Parent Element(s)
-**`input`** `double` Handles input values
-**`process`** `void` Handles process call
-**`reinit`** `void` Handles reinit call
-
-
-#### Shared message fields
-
-Field Type Description
----- ---- ----
-**`proc`** `void` Shared message for process and reinit
-
-
-#### Lookup fields
-
-Field Type Description
----- ---- ----
-**`neighbours`** `string,vector<Id>` Ids of Elements connected this Element on specified field.
-
-
-## testSched
-
-#### Value fields
-
-
-#### Source message fields
-
-
-#### Destination message fields
-
-Field Type Description
----- ---- ----
-**`process`** `void` handles process call
-
-
-#### Shared message fields
-
-
-#### Lookup fields
-
-
-# MOOSE Functions
-
-
-## ce
-Set the current working element. 'ce' is an alias of this function
-
-
-
-## connect
-connect(src, src_field, dest, dest_field, message_type) -> bool
-
-
-
-Create a message between `src_field` on `src` object to `dest_field`
-
-on `dest` object.
-
-
-
-#### Parameters
-
-src : element
-
-the source object
-
-src_field : str
-
-the source field name. Fields listed under `srcFinfo` and
-
-`sharedFinfo` qualify for this.
-
-dest : element
-
-the destination object.
-
-dest_field : str
-
-the destination field name. Fields listed under `destFinfo`
-
-and `sharedFinfo` qualify for this.
-
-message_type : str (optional)
-
-Type of the message. Can be `Single`, `OneToOne`, `OneToAll`.
-
-If not specified, it defaults to `Single`.
-
-
-
-#### Returns
-
-element of the message-manager for the newly created message.
-
-
-
-#### Example
-
-Connect the output of a pulse generator to the input of a spike
-
-generator:
-
-
-
-~~~~
-
->>> pulsegen = moose.PulseGen('pulsegen')
-
->>> spikegen = moose.SpikeGen('spikegen')
-
->>> moose.connect(pulsegen, 'outputOut', spikegen, 'Vm')
-
-1
-
-~~~~
-
-
-
-## copy
-copy(src, dest, name, n, toGlobal, copyExtMsg) -> bool
-
-Make copies of a moose object.
-
-#### Parameters
-
-src : ematrix, element or str
-
-source object.
-
-dest : ematrix, element or str
-
-Destination object to copy into.
-
-name : str
-
-Name of the new object. If omitted, name of the original will be used.
-
-n : int
-
-Number of copies to make.
-
-toGlobal: int
-
-Relevant for parallel environments only. If false, the copies will
-
-reside on local node, otherwise all nodes get the copies.
-
-copyExtMsg: int
-
-If true, messages to/from external objects are also copied.
-
-
-
-#### Returns
-
-ematrix of the copied object
-
-
-
-## delete
-moose.delete(id)
-
-
-
-Delete the underlying moose object. This does not delete any of the
-
-Python objects referring to this ematrix but does invalidate them. Any
-
-attempt to access them will raise a ValueError.
-
-
-
-Parameters
-
-####
-
-id : ematrix
-
-ematrix of the object to be deleted.
-
-
-
-## element
-moose.element(arg) -> moose object
-
-
-
-Convert a path or an object to the appropriate builtin moose class
-
-instance
-
-#### Parameters
-
-arg: str or ematrix or moose object
-
-path of the moose element to be converted or another element (possibly
-
-available as a superclass instance).
-
-
-
-#### Returns
-
-An element of the moose builtin class the specified object belongs
-
-to.
-
-
-
-## exists
-True if there is an object with specified path.
-
-
-
-## getCwe
-Get the current working element. 'pwe' is an alias of this function.
-
-
-
-## getField
-getField(element, field, fieldtype) -- Get specified field of specified type from object ematrix.
-
-
-
-## getFieldDict
-getFieldDict(className, finfoType) -> dict
-
-
-
-Get dictionary of field names and types for specified class.
-
-#### Parameters
-
-className : str
-
-MOOSE class to find the fields of.
-
-finfoType : str (optional)
-
-Finfo type of the fields to find. If empty or not specified, all
-
-fields will be retrieved.
-
-note: This behaviour is different from `getFieldNames` where only
-
-`valueFinfo`s are returned when `finfoType` remains unspecified.
-
-
-
-#### Example
-
-List all the source fields on class Neutral:
-
-~~~~
-
->>> moose.getFieldDict('Neutral', 'srcFinfo')
-
-{'childMsg': 'int'}
-
-~~~~
-
-
-
-## getFieldNames
-getFieldNames(className, finfoType='valueFinfo') -> tuple
-
-
-
-Get a tuple containing the name of all the fields of `finfoType`
-
-kind.
-
-
-
-#### Parameters
-
-className : string
-
-Name of the class to look up.
-
-finfoType : string
-
-The kind of field (`valueFinfo`, `srcFinfo`, `destFinfo`,
-
-`lookupFinfo`, `fieldElementFinfo`.).
-
-
-
-## isRunning
-True if the simulation is currently running.
-
-
-
-## loadModel
-loadModel(filename, modelpath, solverclass) -> moose.ematrix
-
-
-
-Load model from a file to a specified path.
-
-
-
-
-
-#### Parameters
-
-filename : str
-
-model description file.
-
-modelpath : str
-
-moose path for the top level element of the model to be created.
-
-solverclass : str
-
-(optional) solver type to be used for simulating the model.
-
-
-
-#### Returns
-
-ematrix instance refering to the loaded model container.
-
-
-
-## move
-Move a ematrix object to a destination.
-
-
-
-## quit
-Finalize MOOSE threads and quit MOOSE. This is made available for debugging purpose only. It will automatically get called when moose module is unloaded. End user should not use this function.
-
-
-
-## reinit
-reinit() -> None
-
-
-
-Reinitialize simulation.
-
-
-
-This function (re)initializes moose simulation. It must be called
-
-before you start the simulation (see moose.start). If you want to
-
-continue simulation after you have called moose.reinit() and
-
-moose.start(), you must NOT call moose.reinit() again. Calling
-
-moose.reinit() again will take the system back to initial setting
-
-(like clear out all data recording tables, set state variables to
-
-their initial values, etc.
-
-
-
-## saveModel
-saveModel(source, fileame)
-
-
-
-Save model rooted at `source` to file `filename`.
-
-
-
-
-
-#### Parameters
-
-source: ematrix or element or str
-
-root of the model tree
-
-
-
-filename: str
-
-destination file to save the model in.
-
-
-
-#### Returns
-
-None
-
-
-
-## seed
-moose.seed(seedvalue) -> None
-
-
-
-Reseed MOOSE random number generator.
-
-
-
-
-
-#### Parameters
-
-seed: int
-
-Optional value to use for seeding. If 0, a random seed is
-
-automatically created using the current system time and other
-
-information. If not specified, it defaults to 0.
-
-
-
-## setClock
-Set the dt of a clock.
-
-
-
-## setCwe
-Set the current working element. 'ce' is an alias of this function
-
-
-
-## start
-start(t) -> None
-
-
-
-Run simulation for `t` time. Advances the simulator clock by `t`
-
-time.
-
-
-
-After setting up a simulation, YOU MUST CALL MOOSE.REINIT() before
-
-CALLING MOOSE.START() TO EXECUTE THE SIMULATION. Otherwise, the
-
-simulator behaviour will be undefined. Once moose.reinit() has been
-
-called, you can call moose.start(t) as many time as you like. This
-
-will continue the simulation from the last state for `t` time.
-
-
-
-
-
-#### Parameters
-
-t : float
-
-duration of simulation.
-
-
-
-#### Returns
-
-None
-
-
-
-#### See also
-
-moose.reinit : (Re)initialize simulation
-
-
-
-## stop
-Stop simulation
-
-
-
-## useClock
-Schedule objects on a specified clock
-
-
-
-## wildcardFind
-moose.wildcardFind(expression) -> tuple of ematrices.
-
-
-
-Find an object by wildcard.
-
-
-
-
-
-#### Parameters
-
-expression: str
-
-MOOSE allows wildcard expressions of the form
-
-{PATH}/{WILDCARD}[{CONDITION}]
-
-where {PATH} is valid path in the element tree.
-
-{WILDCARD} can be `#` or `##`.
-
-`#` causes the search to be restricted to the children of the
-
-element specified by {PATH}.
-
-`##` makes the search to recursively go through all the descendants
-
-of the {PATH} element.
-
-{CONDITION} can be
-
-TYPE={CLASSNAME} : an element satisfies this condition if it is of
-
-class {CLASSNAME}.
-
-ISA={CLASSNAME} : alias for TYPE={CLASSNAME}
-
-CLASS={CLASSNAME} : alias for TYPE={CLASSNAME}
-
-FIELD({FIELDNAME}){OPERATOR}{VALUE} : compare field {FIELDNAME} with
-
-{VALUE} by {OPERATOR} where {OPERATOR} is a comparison operator (=,
-
-!=, >, <, >=, <=).
-
-For example, /mymodel/##[FIELD(Vm)>=-65] will return a list of all
-
-the objects under /mymodel whose Vm field is >= -65.
-
-
-
-## writeSBML
-Export biochemical model to an SBML file.
-
-
-
-## doc
-Display the documentation for class or field in a class.
-
-
-
-#### Parameters
-
-arg: str or moose class or instance of melement or instance of ematrix
-
-
-
-argument can be a string specifying a moose class name and a field
-
-name separated by a dot. e.g., 'Neutral.name'. Prepending `moose.`
-
-is allowed. Thus moose.doc('moose.Neutral.name') is equivalent to
-
-the above.
-
-
-
-argument can also be string specifying just a moose class name or
-
-a moose class or a moose object (instance of melement or ematrix
-
-or there subclasses). In that case, the builtin documentation for
-
-the corresponding moose class is displayed.
-
-
-
-paged: bool
-
-
-
-Whether to display the docs via builtin pager or print and
-
-exit. If not specified, it defaults to False and moose.doc(xyz)
-
-will print help on xyz and return control to command line.
-
-
-
-## getfielddoc
-Get the documentation for field specified by
-
-tokens.
-
-
-
-tokens should be a two element list/tuple where first element is a
-
-MOOSE class name and second is the field name.
-
-
-
-## getmoosedoc
-Retrieve MOOSE builtin documentation for tokens.
-
-
-
-tokens is a list or tuple containing: (classname, [fieldname])
-
-
-
-## le
-List elements.
-
-
-
-#### Parameters
-
-el: str/melement/ematrix/None
-
-The element or the path under which to look. If `None`, children
-
-of current working element are displayed.
-
-
-
-## listmsg
-Return a list containing the incoming and outgoing messages of
-
-the given object.
-
-
-
-## pwe
-Print present working element. Convenience function for GENESIS
-
-users.
-
-
-
-## showfield
-Show the fields of the element, their data types and values in
-
-human readable format. Convenience function for GENESIS users.
-
-
-
-Parameters:
-
-
-
-elem: str/melement instance
-
-Element or path of an existing element.
-
-
-
-field: str
-
-Field to be displayed. If '*', all fields are displayed.
-
-
-
-showtype: bool
-
-If True show the data type of each field.
-
-
-
-## showfields
-Convenience function. Should be deprecated if nobody uses it.
-
-
-
-## showmsg
-Prints the incoming and outgoing messages of the given object.
-
-
-
-## syncDataHandler
-Synchronize data handlers for target.
-
-
-
-Parameter:
-
-target -- target element or path or ematrix.
-
diff --git a/moose-core/Docs/user/markdown/pymoose2walkthrough.markdown b/moose-core/Docs/user/markdown/pymoose2walkthrough.markdown
deleted file mode 100644
index 8acc2b55a88c4f39eda0b6f15135f0e325813e34..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/markdown/pymoose2walkthrough.markdown
+++ /dev/null
@@ -1,714 +0,0 @@
-% Getting started with python scripting for MOOSE
-% Subhasis Ray
-% December 12, 2012
-
-# Introduction
-
-This document describes how to use the `moose` module in Python
-scripts or in an interactive Python shell. It aims to give you
-enough overview to help you start scripting using MOOSE and extract
-farther information that may be required for advanced work.
-Knowledge of Python or programming in general will be helpful. If
-you just want to simulate existing models in one of the supported
-formats, you can fire the MOOSE GUI and locate the model file using
-the `File` menu and load it. The GUI is described
-[here](./MooseGuiDocs.html). The example code in the boxes can be
-entered in a Python shell.
-
-# Importing MOOSE and accessing built-in documentation
-
-In a python script you import modules to access the functionalities
-they provide.
-
-~~~~{.python}
- import moose
-~~~~
-
-This makes the `moose` module available for use in Python. You can
-use Python's built-in `help` function to read the top-level
-documentation for the moose module:
-
-~~~~{.python}
- help(moose)
-~~~~
-
-This will give you an overview of the module. Press `q` to exit
-the pager and get back to the interpreter. You can also access the
-documentation for individual classes and functions this way.
-
-~~~~{.python}
- help(moose.connect)
-~~~~
-
-To list the available functions and classes you can use `dir`
-function[^1].
-
-~~~~{.python}
- dir(moose)
-~~~~
-
-MOOSE has built-in documentation in the C++-source-code independent
-of Python. The `moose` module has a separate `doc` function to
-extract this documentation.
-
-~~~~{.python}
- moose.doc(moose.Compartment)
-~~~~
-
-The class level documentation will show whatever the
-author/maintainer of the class wrote for documentation followed by
-a list of various kinds of fields and their data types. This can be
-very useful in an interactive session.
-
-Each field can have its own detailed documentation, too.
-
-~~~~{.python}
- moose.doc('Compartment.Rm')
-~~~~
-
-Note that you need to put the class-name followed by dot followed
-by field-name within quotes. Otherwise, `moose.doc` will receive
-the field value as parameter and get confused.
-
-# Creating objects and traversing the object hierarchy
-
-Different types of biological entities like neurons, enzymes, etc
-are represented by classes and individual instances of those types
-are objects of those classes. Objects are the building-blocks of
-models in MOOSE. We call MOOSE objects `element` and use object
-and element interchangeably in the context of MOOSE. Elements are
-conceptually laid out in a tree-like hierarchical structure. If you
-are familiar with file system hierarchies in common operating
-systems, this should be simple.
-
-At the top of the object hierarchy sits the `Shell`, equivalent to
-the root directory in UNIX-based systems and represented by the
-path `/`. You can list the existing objects under `/` using the
-`le` function.
-
-~~~~{.python}
- moose.le()
-~~~~
-
-This shows something like:
-
-~~~~{.python}
- Elements under /
- /Msgs
- /clock
- /classes
-~~~~
-
-`Msgs`, `clock` and `classes` are predefined objects in
-MOOSE. And each object can contain other objects inside them. You
-can see them by passing the path of the parent object to `le`.
-
-Entering:
-
-~~~~{.python}
- moose.le('/clock')
-~~~~
-
-prints:
-
-~~~~{.python}
- Elements under /clock
- /clock/tick[0]
-~~~~
-
-Now let us create some objects of our own. This can be done by
-invoking MOOSE class constructors (just like regular Python
-classes).
-
-~~~~{.python}
- model = moose.Neutral('/model')
-~~~~
-
-The above creates a `Neutral` object named `model`. `Neutral` is
-the most basic class in MOOSE. A `Neutral` element can act as a
-container for other elements. We can create something under
-`model`:
-
-~~~~{.python}
- soma = moose.Compartment('/model/soma')
-~~~~
-
-Every element has a unique path. This is a concatenation of the
-names of all the objects one has to traverse starting with the root
-to reach that element.
-
-~~~~{.python}
- print soma.path
-~~~~
-
-shows you its path:
-
-~~~~{.python}
- /model/soma
-~~~~
-
-The name of the element can be printed, too.
-
-~~~~{.python}
- print soma.name
-~~~~
-
-shows:
-
-~~~~{.python}
- soma
-~~~~
-
-The `Compartment` elements model small portions of a neuron. Some
-basic experiments can be carried out using a single compartment.
-Let us create another object to act on the `soma`. This will be a
-step current generator to inject a current pulse into the soma.
-
-~~~~{.python}
- pulse = moose.PulseGen('/model/pulse')
-~~~~
-
-You can use `le` at any point to see what is there:
-
-~~~~{.python}
- moose.le('/model')
-~~~~
-
-will show you:
-
-~~~~{.python}
- Elements under /model
- /model/soma
- /model/pulse
-~~~~
-
-And finally, we can create a `Table` to record the time series of
-the soma's membrane potential. It is good practice to organize the
-data separately from the model. So we do it as below:
-
-~~~~{.python}
- data = moose.Neutral('/data')
- vmtab = moose.Table('/data/soma_Vm')
-~~~~
-
-Now that we have the essential elements for a small model, we can
-go on to set the properties of this model and the experimental
-protocol.
-
-# Setting the properties of elements: accessing fields
-
-Elements have several kinds of fields. The simplest ones are the
-`value fields`. These can be accessed like ordinary Python members.
-You can list the available value fields using `getFieldNames`
-function:
-
-~~~~{.python}
- soma.getFieldNames('valueFinfo')
-~~~~
-
-Here `valueFinfo` is the type name for value fields. `Finfo` is
-short form of *field information*. For each type of field there is
-a name ending with `-Finfo`. The above will display the following
-list:
-
-~~~~{.python}
- ('this',
- 'name',
- 'me',
- 'parent',
- 'children',
- 'path',
- 'class',
- 'linearSize',
- 'objectDimensions',
- 'lastDimension',
- 'localNumField',
- 'pathIndices',
- 'msgOut',
- 'msgIn',
- 'Vm',
- 'Cm',
- 'Em',
- 'Im',
- 'inject',
- 'initVm',
- 'Rm',
- 'Ra',
- 'diameter',
- 'length',
- 'x0',
- 'y0',
- 'z0',
- 'x',
- 'y',
- 'z')
-~~~~
-
-Some of these fields are for internal or advanced use, some give
-access to the physical properties of the biological entity we are
-trying to model. Now we are interested in `Cm`, `Rm`, `Em` and
-`initVm`. In the most basic form, a neuronal compartment acts like
-a parallel `RC` circuit with a battery attached. Here `R` and `C`
-are resistor and capacitor connected in parallel, and the battery
-with voltage `Em` is in series with the resistor, as shown below:
-
-----
-
-
-
-----
-
-The fields are populated with some defaults.
-
-~~~~{.python}
- print soma.Cm, soma.Rm, soma.Vm, soma.Em, soma.initVm
-~~~~
-
-will give you:
-
-~~~~{.python}
- 1.0 1.0 -0.06 -0.06 -0.06
-~~~~
-
-You can set the `Cm` and `Rm` fields to something realistic using
-simple assignment (we follow SI unit)[^2].
-
-~~~~{.python}
- soma.Cm = 1e-9
- soma.Rm = 1e7
- soma.initVm = -0.07
-~~~~
-
-Instead of writing print statements for each field, you could use
-the utility function showfield to see that the changes took
-effect:
-
-~~~~{.python}
- moose.showfield(soma)
-~~~~
-
-will list most of the fields with their values:
-
-~~~~{.c}
- [ /model/soma ]
- diameter = 0.0
- linearSize = 1
- localNumField = 0
- Ra = 1.0
- y0 = 0.0
- Rm = 10000000.0
- inject = 0.0
- Em = -0.06
- initVm = -0.07
- x = 0.0
- path = /model/soma
- x0 = 0.0
- z0 = 0.0
- class = Compartment
- name = soma
- Cm = 1e-09
- Vm = -0.06
- length = 0.0
- Im = 0.0
- y = 0.0
- lastDimension = 0
- z = 0.0
-~~~~{.python}
-
-Now we can setup the current pulse to be delivered to the soma:
-
-~~~~{.python}
- pulse.delay[0] = 50e-3
- pulse.width[0] = 100e-3
- pulse.level[0] = 1e-9
- pulse.delay[1] = 1e9
-~~~~
-
-This tells the pulse generator to create a 100 ms long pulse 50 ms
-after the start of the simulation. The amplitude of the pulse is
-set to 1 nA. We set the delay for the next pulse to a very large
-value (larger than the total simulation time) so that the
-stimulation stops after the first pulse. Had we set
-`pulse.delay = 0` , it would have generated a pulse train at 50 ms
-intervals.
-
-# Putting them together: setting up connections
-
-In order for the elements to interact during simulation, we need to
-connect them via messages. Elements are connected to each other
-using special source and destination fields. These types are named
-`srcFinfo` and `destFinfo`. You can query the available source and
-destination fields on an element using `getFieldNames` as before.
-This time, let us do it another way: by the class name:
-
-~~~~{.python}
- moose.getFieldNames('PulseGen', 'srcFinfo')
-~~~~
-
-This form has the advantage that you can get information about a
-class without creating elements of that class. The above code
-shows:
-
-~~~~{.python}
- ('childMsg', 'outputOut')
-~~~~
-
-Here `childMsg` is a source field that is used by the MOOSE
-internals to connect child elements to parent elements. The second
-one is of our interest. Check out the built-in documentation here:
-
-~~~~{.python}
- moose.doc('PulseGen.outputOut')
-~~~~
-
-shows:
-
-~~~~{.python}
- PulseGen.outputOut: double - source field
- Current output level.
-~~~~
-
-so this is the output of the pulse generator and this must be
-injected into the `soma` to stimulate it. But where in the `soma`
-can we send it? Again, MOOSE has some introspection built in.
-
-~~~~{.python}
- soma.getFieldNames('destFinfo')
-~~~~
-
-shows:
-
-~~~~{.python}
- ('parentMsg',
- 'set_this',
- 'get_this',
- ...
- 'set_z',
- 'get_z',
- 'injectMsg',
- 'randInject',
- 'cable',
- 'process',
- 'reinit',
- 'initProc',
- 'initReinit',
- 'handleChannel',
- 'handleRaxial',
- 'handleAxial')
-~~~~
-
-Now that is a long list. But much of it are fields for internal or
-special use. Anything that starts with `get_` or `set_` are
-internal `destFinfo` used for accessing value fields (we shall use
-one of those when setting up data recording). Among the rest
-`injectMsg` seems to be the most likely candidate. Use the
-`connect` function to connect the pulse generator output to the
-soma input:
-
-~~~~{.python}
- m = moose.connect(pulse, 'outputOut', soma, 'injectMsg')
-~~~~
-
-`connect(source, source_field, dest, dest_field)` creates a
-`message` from `source` element's `source_field` field to `dest`
-elements `dest_field` field and returns that message. Messages are
-also elements. You can print them to see their identity:
-
-~~~~{.python}
- print m
-~~~~
-
-on my system gives:
-
-~~~~{.python}
- <moose.SingleMsg: id=5, dataId=733, path=/Msgs/singleMsg[733]>
-~~~~
-
-You can print any element as above and the string representation
-will show you the class, two numbers(`id` and `dataId`) uniquely
-identifying it among all elements, and its path. You can get some
-more information about a message:
-
-~~~~{.python}
- print m.e1.path, m.e2.path, m.srcFieldsOnE1, m.destFieldsOnE2
-~~~~
-
-will confirm what you already know:
-
-~~~~{.python}
- /model/pulse /model/soma ('outputOut',) ('injectMsg',)
-~~~~
-
-A message element has fields `e1` and `e2` referring to the
-elements it connects. For single one-directional messages these are
-source and destination elements, which are `pulse` and `soma`
-respectively. The next two items are lists of the field names which
-are connected by this message.
-
-You could also check which elements are connected to a particular
-field:
-
-~~~~{.python}
- print soma.neighbours['injectMsg']
-~~~~
-
-shows:
-
-~~~~{.python}
- [<moose.ematrix: class=PulseGen, id=729,path=/model/pulse>]
-~~~~
-
-Notice that the list contains something called ematrix. We discuss
-this [later](#some-more-details). Also `neighbours` is a new kind of field:
-`lookupFinfo` which behaves like a dictionary. Next we connect the
-table to the soma to retrieve its membrane potential `Vm`. This is
-where all those `destFinfo` starting with `get_` or `set_` come in
-use. For each value field `X`, there is a `destFinfo` `get_{X}`
-to retrieve the value at simulation time. This is used by the table
-to record the values `Vm` takes.
-
-~~~~{.python}
- moose.connect(vmtab, 'requestData', soma, 'get_Vm')
-~~~~
-
-This finishes our model and recording setup. You might be wondering
-about the source-destination relationship above. It is natural to
-think that `soma` is the source of `Vm` values which should be sent
-to `vmtab`. But here `requestData` is a `srcFinfo` acting like a
-reply card. This mode of obtaining data is called *pull*
-mode.[^3]
-
-# Scheduling and running the simulation
-
-With the model all set up, we have to schedule the simulation.
-MOOSE has a central clock element (`/clock`) to manage time. Clock
-has a set of `Tick` elements under it that take care of advancing
-the state of each element with time as the simulation progresses.
-Every element to be included in a simulation must be assigned a
-tick. Each tick can have a different ticking interval (`dt`) that
-allows different elements to be updated at different rates. We
-initialize the ticks and set their `dt` values using the `setClock`
-function.
-
-~~~~{.python}
- moose.setClock(0, 0.025e-3)
- moose.setClock(1, 0.025e-3)
- moose.setClock(2, 0.25e-3)
-~~~~
-
-This will initialize tick #0 and tick #1 with `dt = 25` μs and tick
-#2 with `dt = 250` μs. Thus all the elements scheduled on ticks
-#0 and 1 will be updated every 25 μs and those on tick #2
-every 250 μs. We use the faster clocks for the model components
-where finer timescale is required for numerical accuracy and the
-slower clock to sample the values of `Vm`.
-
-So to assign tick #2 to the table for recording `Vm`, we pass its
-whole path to the `useClock` function.
-
-~~~~{.python}
- moose.useClock(2, '/data/soma_Vm', 'process')
-~~~~
-
-Read this as "use tick # 2 on the element at path `/data/soma_Vm`
-to call its `process` method at every step". Every class that is
-supposed to update its state or take some action during simulation
-implements a `process` method. And in most cases that is the method
-we want the ticks to call at every time step. A less common method
-is `init`, which is implemented in some classes to interleave
-actions or updates that must be executed in a specific
-order[^4]. The `Compartment` class is one such case where
-a neuronal compartment has to know the `Vm` of its neighboring
-compartments before it can calculate its `Vm` for the next step.
-This is done with:
-
-~~~~{.python}
- moose.useClock(0, soma.path, 'init')
-~~~~
-
-Here we used the `path` field instead of writing the path
-explicitly.
-
-Next we assign tick #1 to process method of everything under
-`/model`.
-
-~~~~{.python}
- moose.useClock(1, '/model/##', 'process')
-~~~~
-
-Here the second argument is an example of wild-card path. The `##`
-matches everything under the path preceding it at any depth. Thus
-if we had some other objects under `/model/soma`, `process` method
-of those would also have been scheduled on tick #1. This is very
-useful for complex models where it is tedious to scheduled each
-element individually. In this case we could have used `/model/#` as
-well for the path. This is a single level wild-card which matches
-only the children of `/model` but does not go farther down in the
-hierarchy.
-
-Once the elements are assigned ticks, we can put the model to its
-initial state using:
-
-~~~~{.python}
- moose.reinit()
-~~~~
-
-You may remember that we had changed initVm from `-0.06` to `-0.07`.
-The reinit call we initialize `Vm` to that value. You can verify
-that:
-
-~~~~{.python}
- print soma.Vm
-~~~~
-
-gives:
-
-~~~~{.python}
- -0.07
-~~~~
-
-Finally, we run the simulation for 300 ms:
-
-~~~~{.python}
- moose.start(300e-3)
-~~~~
-
-The data will be recorded by the `soma_vm` table, which is
-referenced by the variable `vmtab`. The `Table` class provides a
-numpy array interface to its content. The field is `vec`. So you
-can easily plot the membrane potential using the
-[matplotlib](http://matplotlib.org/) library.
-
-~~~~{.python}
- import pylab
- t = pylab.linspace(0, 300e-3, len(vmtab.vec))
- pylab.plot(t, vmtab.vec)
- pylab.show()
-~~~~
-
-The first line imports the pylab submodule from matplotlib. This
-useful for interactive plotting. The second line creates the time
-points to match our simulation time and length of the recorded
-data. The third line plots the `Vm` and the fourth line makes it
-visible. Does the plot match your expectation?
-
-# Some more details
-
-## `ematrix`, `melement` and `element`
-
-MOOSE elements are instances of the class `melement`.
-`Compartment`, `PulseGen` and other MOOSE classes are derived
-classes of `melement`. All `melement` instances are contained in
-array-like structures called `ematrix`. Each `ematrix` object has a
-numerical `id_` field uniquely identifying it. An `ematrix` can
-have one or more elements. You can create an array of elements:
-
-~~~~{.python}
- comp_array = moose.ematrix('/model/comp', (3,), 'Compartment')
-~~~~
-
-This tells MOOSE to create an `ematrix` of 3 `Compartment` elements
-with path `/model/comp`. For `ematrix` objects with multiple
-elements, the index in the `ematrix` is part of the element path.
-
-~~~~{.python}
- print comp_array.path, type(comp_array)
-~~~~
-
-shows that `comp_array` is an instance of `ematrix` class. You can
-loop through the elements in an `ematrix` like a Python list:
-
-~~~~{.python}
- for comp in comp_array:
- print comp.path, type(comp)
-~~~~
-
-shows:
-
-~~~~{.python}
- /model/comp[0] <type 'moose.melement'>
- /model/comp[1] <type 'moose.melement'>
- /model/comp[2] <type 'moose.melement'>
-~~~~
-
-Thus elements are instances of class `melement`. All elements in an
-`ematrix` share the `id_` of the `ematrix` which can retrieved by
-`melement.getId()`.
-
-A frequent use case is that after loading a model from a file one
-knows the paths of various model components but does not know the
-appropriate class name for them. For this scenario there is a
-function called `element` which converts ("casts" in programming
-jargon) a path or any moose object to its proper MOOSE class. You
-can create additional references to `soma` in the example this
-way:
-
-~~~~{.python}
- x = moose.element('/model/soma')
-~~~~
-
-Any MOOSE class can be extended in Python. But any additional
-attributes added in Python are invisible to MOOSE. So those can be
-used for functionalities at the Python level only. You can see
-`Demos/squid/squid.py` for an example.
-
-## `Finfos`
-
-The following kinds of `Finfo` are accessible in Python
-
-- **`valueFinfo`** :
- simple values. For each readable `valueFinfo` `XYZ` there is a
- `destFinfo` `get_XYZ` that can be used for reading the value at run
- time. If `XYZ` is writable then there will also be `destFinfo` to
- set it: `set_XYZ`. Example: `Compartment.Rm`
-- **`lookupFinfo`** :
- lookup tables. These fields act like Python dictionaries but
- iteration is not supported. Example: `Neutral.neighbours`.
-- **`srcFinfo`** :
- source of a message. Example: `PulseGen.outputOut`.
-- **`destFinfo`** :
- destination of a message. Example: `Compartment.injectMsg`.
- Apart from being used in setting up messages, these are accessible
- as functions from Python. `HHGate.setupAlpha` is an example.
-- **`sharedFinfo`** :
- a composition of source and destination fields. Example:
- `Compartment.channel`.
-
-# Moving on
-
-Now you know the basics of pymoose and how to access the help
-system. MOOSE is backward compatible with GENESIS and most GENESIS
-classes have been reimplemented in MOOSE. There is slight change in
-naming (MOOSE uses CamelCase), and setting up messages are
-different. But
-[GENESIS documentation](http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual.html)
-is still a good source for documentation on classes that have been
-ported from GENESIS.
-
-In addition, the `Demos/snippets` directory in your MOOSE
-installation has small executable python scripts that show usage of
-specific classes or functionalities. Beyond that you can browse the
-code in the `Demos` directory to see some more complex models.
-
-If the built-in MOOSE classes do not satisfy your needs entirely,
-you are welcome to add new classes to MOOSE. The
-API documentation will help you get started. Finally
-you can join the
-[moose mailing list](https://lists.sourceforge.net/lists/listinfo/moose-generic)
-and request for help.
-
-[^1]: To list the classes only, use `moose.le('/classes')`
-
-[^2]: MOOSE is unit agnostic and things should work fine
-as long as you use values all converted to a consistent unit
-system.
-
-[^3]: This apparently convoluted implementation is for
-performance reason. Can you figure out why?
-*Hint: the table is driven by a slower clock than the compartment.*
-
-[^4]: In principle any function available in a MOOSE class
-can be executed periodically this way as long as that class exposes
-the function for scheduling following the MOOSE API. So you have to
-consult the class' documentation for any nonstandard methods that
-can be scheduled this way.
diff --git a/moose-core/Docs/user/py/Makefile b/moose-core/Docs/user/py/Makefile
deleted file mode 100644
index 182070907cae692fced766d21141b1ccbc52a887..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/Makefile
+++ /dev/null
@@ -1,153 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-PAPER =
-BUILDDIR = _build
-
-# Internal variables.
-PAPEROPT_a4 = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
-help:
- @echo "Please use \`make <target>' where <target> is one of"
- @echo " html to make standalone HTML files"
- @echo " dirhtml to make HTML files named index.html in directories"
- @echo " singlehtml to make a single large HTML file"
- @echo " pickle to make pickle files"
- @echo " json to make JSON files"
- @echo " htmlhelp to make HTML files and a HTML help project"
- @echo " qthelp to make HTML files and a qthelp project"
- @echo " devhelp to make HTML files and a Devhelp project"
- @echo " epub to make an epub"
- @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
- @echo " latexpdf to make LaTeX files and run them through pdflatex"
- @echo " text to make text files"
- @echo " man to make manual pages"
- @echo " texinfo to make Texinfo files"
- @echo " info to make Texinfo files and run them through makeinfo"
- @echo " gettext to make PO message catalogs"
- @echo " changes to make an overview of all changed/added/deprecated items"
- @echo " linkcheck to check all external links for integrity"
- @echo " doctest to run all doctests embedded in the documentation (if enabled)"
-
-clean:
- -rm -rf $(BUILDDIR)/*
-
-html:
- $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
- $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
- $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
- @echo
- @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
- $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
- @echo
- @echo "Build finished; now you can process the pickle files."
-
-json:
- $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
- @echo
- @echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
- $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
- @echo
- @echo "Build finished; now you can run HTML Help Workshop with the" \
- ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
- $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
- @echo
- @echo "Build finished; now you can run "qcollectiongenerator" with the" \
- ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
- @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/MOOSE.qhcp"
- @echo "To view the help file:"
- @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/MOOSE.qhc"
-
-devhelp:
- $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
- @echo
- @echo "Build finished."
- @echo "To view the help file:"
- @echo "# mkdir -p $$HOME/.local/share/devhelp/MOOSE"
- @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/MOOSE"
- @echo "# devhelp"
-
-epub:
- $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
- @echo
- @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-latex:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo
- @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
- @echo "Run \`make' in that directory to run these through (pdf)latex" \
- "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo "Running LaTeX files through pdflatex..."
- $(MAKE) -C $(BUILDDIR)/latex all-pdf
- @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text:
- $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
- @echo
- @echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man:
- $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
- @echo
- @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo
- @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
- @echo "Run \`make' in that directory to run these through makeinfo" \
- "(use \`make info' here to do that automatically)."
-
-info:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo "Running Texinfo files through makeinfo..."
- make -C $(BUILDDIR)/texinfo info
- @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext:
- $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
- @echo
- @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes:
- $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
- @echo
- @echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck:
- $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
- @echo
- @echo "Link check complete; look for any errors in the above output " \
- "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest:
- $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
- @echo "Testing of doctests in the sources finished, look at the " \
- "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/moose-core/Docs/user/py/README.txt b/moose-core/Docs/user/py/README.txt
deleted file mode 100644
index 39f11b6deed42cd3ce0f3c16fee53797725d526d..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/README.txt
+++ /dev/null
@@ -1,29 +0,0 @@
-This directory contains MOOSE user documentation in reST format that can be
-compiled into various formats by sphinx. To build the documentation in HTML,
-format enter the command:
-
-make html
-
-in this directory. Then you can open _build/html/index.html in browser to
-browse the generated documentation.
-
-Every MOOSE class has builtin documentation. This can be extracted into a
-reST file by running the script:
-
- python create_all_rst_doc.py
-
-This process must be carried out before making the docs after any
-change in the built-in documentation is compiled into MOOSE.
-
-Other files
- - conf.py: the Sphinx configuration file.
- - index.rst: This is the index file for use when building the Python
- docs using sphinx.
- - moose_quickstart.rst: A walk-through of basic usage of moose.
- - moose_cookbook.rst: Recipes for specific tasks in moose.
- - moose_builtins.rst: This is for sphinx to process the pymoose builtin
- doc strings (using autodoc extension).
- - moose_classes.rst: The Python docs extracted above using
- create_all_rst_doc.py
-
-
diff --git a/moose-core/Docs/user/py/_templates/layout.html b/moose-core/Docs/user/py/_templates/layout.html
deleted file mode 100644
index b1b5618573a72a0fe082158b72db2c582c7dbaea..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/_templates/layout.html
+++ /dev/null
@@ -1,33 +0,0 @@
-{% extends "!layout.html" %}
-{% block rootrellink %}
- <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li>
- {{ super() }}
-{% endblock %}
-{% block sidebartitle %}
-
- {% if logo and theme_logo_only %}
- <a href="{{ pathto(master_doc) }}">
- {% else %}
- <a href="http://moose.ncbs.res.in/" class="icon icon-home"> {{ project }}
- {% endif %}
-
- {% if logo %}
- {# Not strictly valid HTML, but it's the only way to display/scale it properly, without weird scripting or heaps of work #}
- <img src="{{ pathto('_static/' + logo, 1) }}" class="logo" />
- {% endif %}
- </a>
- {% if theme_display_version %}
- {%- set nav_version = version %}
- {% if READTHEDOCS and current_version %}
- {%- set nav_version = current_version %}
- {% endif %}
- {% if nav_version %}
- <div class="version">
- {{ nav_version }}
- </div>
- {% endif %}
- {% endif %}
-
- {% include "searchbox.html" %}
-{% endblock %}
-
diff --git a/moose-core/Docs/user/py/conf.py b/moose-core/Docs/user/py/conf.py
deleted file mode 100644
index b177111f6e7f7ae91c3c4c2808e0283d659005ca..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/conf.py
+++ /dev/null
@@ -1,257 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# MOOSE documentation build configuration file, created by
-# sphinx-quickstart on Tue Jul 1 19:05:47 2014.
-# updated on Thr Jan 21 00:30:10 2016
-# This file is execfile()d with the current directory set to its containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-import sys, os
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('../../../python'))
-sys.path.append(os.path.abspath('../../../../moose-examples/snippets'))
-sys.path.append(os.path.abspath('../../../../moose-examples/tutorials/ChemicalOscillators'))
-sys.path.append(os.path.abspath('../../../../moose-examples/tutorials/ChemicalBistables'))
-sys.path.append(os.path.abspath('../../../../moose-examples/tutorials/ExcInhNet'))
-sys.path.append(os.path.abspath('../../../../moose-examples/neuroml/lobster_pyloric'))
-sys.path.append(os.path.abspath('../../../../moose-examples/tutorials/ExcInhNetCaPlasticity'))
-
-# -- General configuration -----------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be extensions
-# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc',
- 'sphinx.ext.mathjax',
- 'sphinx.ext.autosummary',
- 'sphinx.ext.viewcode',
- 'numpydoc'
- ]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix of source filenames.
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8-sig'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'MOOSE'
-copyright = u'2016, Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray, Harsha Rani and Dilawar Singh'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '3.2'
-# The full version, including alpha/beta/rc tags.
-release = '3.2'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#language = None
-
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns = ['_build']
-
-# The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-
-# -- Options for HTML output ---------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages. See the documentation for
-# a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
-#html_theme = 'default'
-# Theme options are theme-specific and customize the look and feel of a theme
-# further. For a list of options available for each theme, see the
-# documentation.
-# html_theme_options = {'stickysidebar': 'true',
-# 'sidebarwidth': '300'}
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
-# The name for this set of Sphinx documents. If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-html_logo = '../../images/moose_logo.png'
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-#html_domain_indices = True
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
-
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it. The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'MOOSEdoc'
-
-
-# -- Options for LaTeX output --------------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
- ('index', 'MOOSE.tex', u'MOOSE Documentation',
- u'Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray,Harsha Rani and Dilawar Singh', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-latex_logo = 'images/moose_logo.png'
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-latex_show_pagerefs = True
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-latex_domain_indices = True
-
-
-# -- Options for manual page output --------------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
- ('index', 'moose', u'MOOSE Documentation',
- [u'Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray,Harsha Rani and Dilawar Singh'], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output ------------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-# dir menu entry, description, category)
-texinfo_documents = [
- ('index', 'MOOSE', u'MOOSE Documentation',
- u'Upinder Bhalla, Niraj Dudani, Aditya Gilra, Aviral Goel, Subhasis Ray,Harsha Rani and Dilawar Singh', 'MOOSE', 'MOOSE is the Multiscale Object-Oriented Simulation Environment.',
- 'Science'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-#numpydoc option
-numpydoc_show_class_members = True
diff --git a/moose-core/Docs/user/py/create_all_rstdoc.py b/moose-core/Docs/user/py/create_all_rstdoc.py
deleted file mode 100644
index 5f0af2aa2e847949786b98028058eb9e281c100d..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/create_all_rstdoc.py
+++ /dev/null
@@ -1,277 +0,0 @@
-# create_all_rstdoc.py ---
-#
-# Filename: create_all_rstdoc.py
-# Description:
-# Author: Subhasis Ray
-# Maintainer:
-# Created: Mon Jun 30 21:35:07 2014 (+0530)
-# Version:
-# Last-Updated:
-# By:
-# Update #: 0
-# URL:
-# Keywords:
-# Compatibility:
-#
-#
-
-# Commentary:
-#
-#
-#
-#
-
-# Change log:
-#
-#
-#
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License as
-# published by the Free Software Foundation; either version 3, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; see the file COPYING. If not, write to
-# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
-# Floor, Boston, MA 02110-1301, USA.
-#
-#
-
-# Code:
-"""Dump reStructuredText of moose builtin class docs as well as those
-built into pymoose and moose python scripts."""
-
-import sys
-sys.path.append('../../../python')
-import cStringIO
-import re
-import inspect
-from datetime import datetime
-import pydoc
-import moose
-
-# We assume any non-word-constituent character in the start of C++
-# type name to be due to the name-mangling done by compiler on
-# templated or user defined types.
-type_mangling_regex = re.compile('^[^a-zA-Z]+')
-
-finfotypes = dict(moose.finfotypes)
-
-def extract_finfo_doc(cinfo, finfotype, docio, indent=' '):
- """Extract field documentation for all fields of type `finfotype`
- in class `cinfo` into `docio`.
-
- Parameters
- ----------
- cinfo: moose.Cinfo
- class info object in MOOSE.
-
- ftype: str
- finfo type (valueFinfo/srcFinfo/destFinfo/lookupFinfo/sharedFinfo
-
- docio: StringIO
- IO object to write the documentation into
- """
- data = []
- try:
- finfo = moose.element('%s/%s' % (cinfo.path, finfotype)).vec
- except ValueError:
- return
- for field_element in finfo:
- dtype = type_mangling_regex.sub('', field_element.type)
- if len(dtype.strip()) == 0:
- dtype = 'void'
- if finfotype.startswith('dest'):
- name = '.. py:method:: {0}'.format(field_element.fieldName)
- dtype = ''
- else:
- name = '.. py:attribute:: {0}'.format(field_element.fieldName)
- dtype = '{0}'.format(dtype)
- doc = field_element.docs.replace('_', '\\_')
-
- docio.write('{0}{1}\n\n'.format(indent, name).replace('_', '\\_'))
- ftype = '{0} (*{1}*)\n\n'.format(dtype, finfotypes[finfotype]).strip()
- docio.write('{0} {1}'.format(indent, ftype))
- for line in doc.split('\n'):
- docio.write('{0} {1}\n'.format(indent, line))
- docio.write('\n\n')
-
-def extract_class_doc(name, docio, indent=' '):
- """Extract documentation for Cinfo object at path
-
- Parameters
- ----------
- name: str
- path of the class.
-
- docio: StringIO
- output object to write the documentation into.
- """
- cinfo = moose.Cinfo('/classes/%s' % (name))
- docs = cinfo.docs
- docio.write('{0}.. py:class:: {1}\n\n'.format(indent, cinfo.name).replace('_', '\\_'))
- if docs:
- docs = docs.split('\n')
- # We need these checks to avoid mis-processing `:` within
- # description of the class
- name_done = False
- author_done = False
- descr_done = False
- for doc in docs:
- if not doc:
- continue
- field = None
- if not (name_done and author_done and descr_done):
- pos = doc.find(':')
- field = doc[:pos]
- if field.lower() == 'name':
- name_done = True
- continue
- elif field.lower() == 'author':
- author_done = True
- continue
- elif field.lower() == 'description':
- descr_done = True
- content = doc[pos+1:].strip()
- else:
- content = doc
- content = content.replace('_', '\\_')
- docio.write('{0} {1}\n'.format(indent, content))
- docio.write('\n')
- for finfotype in finfotypes.keys():
- extract_finfo_doc(cinfo, finfotype, docio, indent + ' ')
-
-def extract_all_class_doc(docio, indent=' '):
- for cinfo in moose.element('/classes').children:
- extract_class_doc(cinfo.name, docio, indent=indent)
-
-def extract_all_func_doc(docio, indent=' '):
- for fname, fdef in (inspect.getmembers(moose, inspect.isbuiltin) +
- inspect.getmembers(moose, inspect.isfunction)):
- docio.write('\n{}.. py:func:: {}\n'.format(indent, fname).replace('_', '\\_'))
- doc = inspect.getdoc(fdef)
- doc = doc.split('\n')
- drop = []
- for i in range(len(doc)):
- di = doc[i]
- doc[i] = di
- hyphen_count = di.count('-')
- if hyphen_count > 0 and hyphen_count == len(di) and i > 0:
- drop.append(i)
- doc[i-1] = indent + doc[i-1]
- for i in range(len(doc)):
- if i not in drop:
- docio.write(doc[i].replace('_', '\\_') + '\n\n')
-
-
-if __name__ == '__main__':
- classes_doc = 'moose_classes.rst'
- builtins_doc = 'moose_builtins.rst'
- overview_doc = 'moose_overview.rst'
- if len(sys.argv) > 1:
- classes_doc = sys.argv[1]
- if len(sys.argv) > 2:
- builtins_doc = sys.argv[2]
- if len(sys.argv) > 3:
- overview_doc = sys.argv[3]
- ts = datetime.now()
-
- # # MOOSE overview - the module level doc - this is for extracting
- # # the moose docs into separate component files.
- # overview_docio = open(overview_doc, 'w')
- # overview_docio.write('.. MOOSE overview\n')
- # overview_docio.write('.. As visible in the Python module\n')
- # overview_docio.write(ts.strftime('.. Auto-generated on %B %d, %Y\n'))
- # overview_docio.write('\n'.join(pydoc.getdoc(moose).split('\n')).replace('_', '\\_'))
- # overview_docio.write('\n')
-
-
- # if isinstance(overview_docio, cStringIO.OutputType):
- # print overview_docio.getvalue()
- # else:
- # overview_docio.close()
-
- ## Builtin docs - we are going to do something like what autodoc
- ## does for sphinx. Because we cannot afford to build moose on
- ## servers like readthedocs, we ourselvs ectract the docs into rst
- ## files.
-# builtins_docio = open(builtins_doc, 'w')
-# builtins_docio.write('.. Documentation for all MOOSE builtin functions\n')
-# builtins_docio.write('.. As visible in the Python module\n')
-# builtins_docio.write(ts.strftime('.. Auto-generated on %B %d, %Y\n'))
-# builtins_docio.write('''
-
-# # MOOSE Builitin Classes and Functions
-# # ====================================
-# # ''')
-# builtins_docio.write('\n.. py:module:: moose\n')
-# indent = ' '
-# for item in ['vec', 'melement', 'LookupField', 'DestField', 'ElementField']:
-# builtins_docio.write('\n\n{0}.. py:class:: {1}\n'.format(indent, item).replace('_', '\\_'))
-# class_obj = eval('moose.{0}'.format(item))
-# doc = pydoc.getdoc(class_obj).replace('_', '\\_')
-# for line in doc.split('\n'):
-# builtins_docio.write('\n{0}{0}{1}'.format(indent, line))
-# for name, member in inspect.getmembers(class_obj):
-# if name.startswith('__'):
-# continue
-# if inspect.ismethod(member) or inspect.ismethoddescriptor(member):
-# builtins_docio.write('\n\n{0}{0}.. py:method:: {1}\n'.format(indent, name).replace('_', '\\_'))
-# else:
-# builtins_docio.write('\n\n{0}{0}.. py:attribute:: {1}\n'.format(indent, name).replace('_', '\\_'))
-# doc = inspect.getdoc(member).replace('_', '\\_')
-# for line in doc.split('\n'):
-# builtins_docio.write('\n{0}{0}{0}{1}'.format(indent, line))
-
-# for item in ['pwe', 'le', 'ce', 'showfield', 'showmsg', 'doc', 'element',
-# 'getFieldNames', 'copy', 'move', 'delete',
-# 'useClock', 'setClock', 'start', 'reinit', 'stop', 'isRunning',
-# 'exists', 'writeSBML', 'readSBML', 'loadModel', 'saveModel',
-# 'connect', 'getCwe', 'setCwe', 'getFieldDict', 'getField',
-# 'seed', 'rand', 'wildcardFind', 'quit']:
-# builtins_docio.write('\n\n{0}.. py:function:: {1}\n'.format(indent, item).replace('_', '\\_'))
-# doc = inspect.getdoc(eval('moose.{0}'.format(item))).replace('_', '\\_')
-# for line in doc.split('\n'):
-# builtins_docio.write('\n{0}{0}{1}'.format(indent, line))
-# builtins_docio.write('\n')
-# if isinstance(builtins_docio, cStringIO.OutputType):
-# print builtins_docio.getvalue()
-# else:
-# builtins_docio.close()
- # This is the primary purpos
- classes_docio = open(classes_doc, 'w')
- classes_docio.write('.. Documentation for all MOOSE classes and functions\n')
- classes_docio.write('.. As visible in the Python module\n')
- classes_docio.write(ts.strftime('.. Auto-generated on %B %d, %Y\n'))
-
- classes_docio.write('''
-
-MOOSE Classes
-==================
-''')
- extract_all_class_doc(classes_docio, indent='')
-# classes_docio.write('''
-# =================
-# MOOSE Functions
-# =================
-# ''')
-# extract_all_func_doc(classes_docio, indent='')
- if isinstance(classes_docio, cStringIO.OutputType):
- print classes_docio.getvalue()
- else:
- classes_docio.close()
-
-
-
-
-
-
-
-#
-# create_all_rstdoc.py ends here
diff --git a/moose-core/Docs/user/py/index.rst b/moose-core/Docs/user/py/index.rst
deleted file mode 100644
index 3a537be188cd9438a3d8b9e993c0f0320cee7c21..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/index.rst
+++ /dev/null
@@ -1,41 +0,0 @@
-.. MOOSE documentation master file, created by
- sphinx-quickstart on Tue Jul 1 19:05:47 2014.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-the Multiscale Object-Oriented Simulation Environment
-=====================================================
-What is MOOSE and what is it good for?
---------------------------------------
-MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed to simulate neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, circuits, and large networks. MOOSE can operate at many levels of detail, from stochastic chemical computations, to multicompartment single-neuron models, to spiking neuron network models.
-
-.. figure:: ../../images/Gallery_Moose_Multiscale.png
- :alt: **multiple scales in moose**
- :scale: 50%
-
- *Multiple scales can be modelled and simulated in MOOSE*
-
-MOOSE is multiscale: It can do all these calculations together. One of its major uses is to make biologically detailed models that combine electrical and chemical signaling.
-
-MOOSE is object-oriented. Biological concepts are mapped into classes, and a model is built by creating instances of these classes and connecting them by messages. MOOSE also has numerical classes whose job is to take over difficult computations in a certain domain, and do them fast. There are such solver classes for stochastic and deterministic chemistry, for diffusion, and for multicompartment neuronal models.
-
-MOOSE is a simulation environment, not just a numerical engine: It provides data representations and solvers (of course!), but also a scripting interface with Python, graphical displays with Matplotlib, PyQt, and OpenGL, and support for many model formats. These include SBML, NeuroML, GENESIS kkit and cell.p formats, HDF5 and NSDF for data writing.
-
-Contents:
-
-.. toctree::
- :maxdepth: 2
- :numbered:
-
- moose_quickstart
- moose_cookbook
- moose_builtins
- moose_classes
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
diff --git a/moose-core/Docs/user/py/make.bat b/moose-core/Docs/user/py/make.bat
deleted file mode 100644
index 78e062d3145df77981900d15f590766a16e566e9..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/make.bat
+++ /dev/null
@@ -1,190 +0,0 @@
-@ECHO OFF
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
- set SPHINXBUILD=sphinx-build
-)
-set BUILDDIR=_build
-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
-set I18NSPHINXOPTS=%SPHINXOPTS% .
-if NOT "%PAPER%" == "" (
- set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
- set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
-)
-
-if "%1" == "" goto help
-
-if "%1" == "help" (
- :help
- echo.Please use `make ^<target^>` where ^<target^> is one of
- echo. html to make standalone HTML files
- echo. dirhtml to make HTML files named index.html in directories
- echo. singlehtml to make a single large HTML file
- echo. pickle to make pickle files
- echo. json to make JSON files
- echo. htmlhelp to make HTML files and a HTML help project
- echo. qthelp to make HTML files and a qthelp project
- echo. devhelp to make HTML files and a Devhelp project
- echo. epub to make an epub
- echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
- echo. text to make text files
- echo. man to make manual pages
- echo. texinfo to make Texinfo files
- echo. gettext to make PO message catalogs
- echo. changes to make an overview over all changed/added/deprecated items
- echo. linkcheck to check all external links for integrity
- echo. doctest to run all doctests embedded in the documentation if enabled
- goto end
-)
-
-if "%1" == "clean" (
- for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
- del /q /s %BUILDDIR%\*
- goto end
-)
-
-if "%1" == "html" (
- %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished. The HTML pages are in %BUILDDIR%/html.
- goto end
-)
-
-if "%1" == "dirhtml" (
- %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
- goto end
-)
-
-if "%1" == "singlehtml" (
- %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
- goto end
-)
-
-if "%1" == "pickle" (
- %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished; now you can process the pickle files.
- goto end
-)
-
-if "%1" == "json" (
- %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished; now you can process the JSON files.
- goto end
-)
-
-if "%1" == "htmlhelp" (
- %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished; now you can run HTML Help Workshop with the ^
-.hhp project file in %BUILDDIR%/htmlhelp.
- goto end
-)
-
-if "%1" == "qthelp" (
- %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished; now you can run "qcollectiongenerator" with the ^
-.qhcp project file in %BUILDDIR%/qthelp, like this:
- echo.^> qcollectiongenerator %BUILDDIR%\qthelp\MOOSE.qhcp
- echo.To view the help file:
- echo.^> assistant -collectionFile %BUILDDIR%\qthelp\MOOSE.ghc
- goto end
-)
-
-if "%1" == "devhelp" (
- %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished.
- goto end
-)
-
-if "%1" == "epub" (
- %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished. The epub file is in %BUILDDIR%/epub.
- goto end
-)
-
-if "%1" == "latex" (
- %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
- goto end
-)
-
-if "%1" == "text" (
- %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished. The text files are in %BUILDDIR%/text.
- goto end
-)
-
-if "%1" == "man" (
- %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished. The manual pages are in %BUILDDIR%/man.
- goto end
-)
-
-if "%1" == "texinfo" (
- %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
- goto end
-)
-
-if "%1" == "gettext" (
- %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
- if errorlevel 1 exit /b 1
- echo.
- echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
- goto end
-)
-
-if "%1" == "changes" (
- %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
- if errorlevel 1 exit /b 1
- echo.
- echo.The overview file is in %BUILDDIR%/changes.
- goto end
-)
-
-if "%1" == "linkcheck" (
- %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
- if errorlevel 1 exit /b 1
- echo.
- echo.Link check complete; look for any errors in the above output ^
-or in %BUILDDIR%/linkcheck/output.txt.
- goto end
-)
-
-if "%1" == "doctest" (
- %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
- if errorlevel 1 exit /b 1
- echo.
- echo.Testing of doctests in the sources finished, look at the ^
-results in %BUILDDIR%/doctest/output.txt.
- goto end
-)
-
-:end
diff --git a/moose-core/Docs/user/py/moose_builtins.rst b/moose-core/Docs/user/py/moose_builtins.rst
deleted file mode 100644
index 579131b82c15fe14ce1d81b374ea702efb0d244d..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/moose_builtins.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-.. Documentation for all MOOSE builtin-functions accessible in python
-.. As visible in the Python module
-.. Created by Subhasis Ray, NCBS, Tue Jul 1 14:41:10 IST 2014
-
-==============
-MOOSE builtins
-==============
-
-This document describes classes and functions specific to the MOOSE
-Python module. This is an API reference.
-
-* If you are looking for basic tutorials for getting started with
- moose, then check :doc:`moose_quickstart`.
-
-* If you want recipes for particular tasks, check out
- :doc:`moose_cookbook`.
-
-* If you want the reference for specific moose classes, then go to
- :doc:`moose_classes`.
-
-
-.. automodule:: moose
- :show-inheritance:
- :members: DestField, ElementField, LookupField, ce, connect, copy, delete, doc, element, exists, getCwe, getField, getFieldDict, getFieldNames, isRunning, le, loadModel, melement, move, pwe, quit, rand, readSBML, reinit, saveModel, seed, setClock, setCwe, showfield, showmsg, start, stop, useClock, vec, wildcardFind, writeSBML
diff --git a/moose-core/Docs/user/py/moose_classes.rst b/moose-core/Docs/user/py/moose_classes.rst
deleted file mode 100644
index c9490cbed134147f8a0b51d0bacc13ca827ad1e4..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/moose_classes.rst
+++ /dev/null
@@ -1,10149 +0,0 @@
-.. Documentation for all MOOSE classes and functions
-.. As visible in the Python module
-.. Auto-generated on October 01, 2014
-
-=============
-MOOSE Classes
-=============
-
-MOOSE builtin classes and their fields are listed here.
-
-
-Alphabetical listing of moose classes
--------------------------------------
-
-.. py:class:: Adaptor
-
- This is the adaptor class. It is used in interfacing different kinds of solver with each other, especially for electrical to chemical signeur models. The Adaptor class is the core of the API for interfacing between different solution engines. It is currently in use for interfacing between chemical and electrical simulations, but could be used for other cases such as mechanical models. The API for interfacing between solution engines rests on the following capabilities of MOOSE:
- 1. The object-oriented interface with classes mapped to biological and modeling concepts such as electrical and chemical compartments, ion channels and molecular pools.
- 2. The invisible mapping of Solvers (Objects implementing numerical engines) to the object-oriented interface. Solvers work behind the scenes to update the objects.
- 3. The messaging interface which allows any visible field to be accessed and updated from any other object.
- 4. The clock-based scheduler which drives operations of any subset of objects at any interval. For example, this permits the operations of field access and update to take place at quite different timescales from the numerical engines.
- 5. The implementation of Adaptor classes. These perform a linear transformation::
- (y = scale * (x + inputOffset) + outputOffset )
- where y is output and x is the input. The input is the average of any number of sources (through messages) and any number of timesteps. The output goes to any number of targets, again through messages.
-
- It is worth adding that messages can transport arbitrary data structures, so it would also be possible to devise a complicated opaque message directly between solvers. The implementation of Adaptors working on visible fields does this much more transparently and gives the user facile control over the scaling transformation. These adaptors are used especially in the rdesigneur framework of MOOSE, which enables multiscale reaction-diffusion and electrical signaling models.
-
- As an example of this API in operation, I consider two mappings:
- 1. Calcium mapped from electrical to chemical computations.
- 2. phosphorylation state of a channel mapped to the channel conductance.
-
- 1. Calcium mapping.
- Problem statement.
- Calcium is computed in the electrical solver as one or more pools that are fed by calcium currents, and is removed by an exponential decay process. This calcium pool is non-diffusive in the current electrical solver. It has to be mapped to chemical calcium pools at a different spatial discretization, which do diffuse.
-
- In terms of the list of capabilities described above, this is how the API works.
- 1. The electrical model is partitioned into a number of electrical compartments, some of which have the 'electrical' calcium pool as child object in a UNIX filesystem-like tree. Thus the 'electrical' calcium is represented as an object with concentration, location and so on.
- 2. The Solver computes the time-course of evolution of the calcium concentration. Whenever any function queries the 'concentration' field of the calcium object, the Solver provides this value.
- 3. Messaging couples the 'electrical' calcium pool concentration to the adaptor (see point 5). This can either be a 'push' operation, where the solver pushes out the calcium value at its internal update rate, or a 'pull' operation where the adaptor requests the calcium concentration.
- 4. The clock-based scheduler keeps the electrical and chemical solvers ticking away, but it also can drive the operations of the adaptor. Thus the rate of updates to and from the adaptor can be controlled.
- 5. The adaptor averages its inputs. Say the electrical solver is going at a timestep of 50 usec, and the chemical solver at 5000 usec. The adaptor will take 100 samples of the electrical concentration, and average them to compute the 'input' to the linear scaling. Suppose that the electrical model has calcium units of micromolar, but has a zero baseline. The chemical model has units of millimolar and a baseline of 1e-4 millimolar. This gives:
- y = 0.001x + 1e-4
- At the end of this calculation, the adaptor will typically 'push' its output to the chemical solver. Here we have similar situation to item (1), where the chemical entities are calcium pools in space, each with their own calcium concentration. The messaging (3) determines another aspect of the mapping here: the fan in or fan out. In this case, a single electrical compartment may house 10 chemical compartments. Then the output message from the adaptor goes to update the calcium pool concentration on the appropriate 10 objects representing calcium in each of the compartments.
-
- In much the same manner, the phosphorylation state can regulate channel properties.
- 1. The chemical model contains spatially distributed chemical pools that represent the unphosphorylated state of the channel, which in this example is the conducting form. This concentration of this unphosphorylated state is affected by the various reaction- diffusion events handled by the chemical solver, below.
- 2. The chemical solver updates the concentrations of the pool objects as per reaction-diffusion calculations.
- 3. Messaging couples these concentration terms to the adaptor. In this case we have many chemical pool objects for every electrical compartment. There would be a single adaptor for each electrical compartment, and it would average all the input values for calcium concentration, one for each mesh point in the chemical calculation. As before, the access to these fields could be through a 'push' or a 'pull' operation.
- 4. The clock-based scheduler oeperates as above. 5. The adaptor averages the spatially distributed inputs from calcium, and now does a different linear transform. In this case it converts chemical concentration into the channel conductance. As before, the 'electrical' channel is an object (point 1) with a field for conductance, and this term is mapped into the internal data structures of the solver (point 2) invisibly to the user.
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process message from the scheduler.
-
-
- .. py:method:: setInputOffset
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInputOffset
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setOutputOffset
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getOutputOffset
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setScale
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getScale
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getOutputValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: input
-
- (*destination message field*) Input message to the adaptor. If multiple inputs are received, the system averages the inputs.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles 'process' call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles 'reinit' call
-
-
- .. py:attribute:: output
-
- double (*source message field*) Sends the output value every timestep.
-
-
- .. py:attribute:: requestOut
-
- PSt6vectorIdSaIdEE (*source message field*) Sends out a request to a field with a double or array of doubles. Issued from the process call.Works for any number of targets.
-
-
- .. py:attribute:: inputOffset
-
- double (*value field*) Offset to apply to input message, before scaling
-
-
- .. py:attribute:: outputOffset
-
- double (*value field*) Offset to apply at output, after scaling
-
-
- .. py:attribute:: scale
-
- double (*value field*) Scaling factor to apply to input
-
-
- .. py:attribute:: outputValue
-
- double (*value field*) This is the linearly transformed output.
-
-
-.. py:class:: Annotator
-
-
- .. py:method:: setX
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNotes
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNotes
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setColor
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getColor
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTextColor
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTextColor
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setIcon
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getIcon
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: x
-
- double (*value field*) x field. Typically display coordinate x
-
-
- .. py:attribute:: y
-
- double (*value field*) y field. Typically display coordinate y
-
-
- .. py:attribute:: z
-
- double (*value field*) z field. Typically display coordinate z
-
-
- .. py:attribute:: notes
-
- string (*value field*) A string to hold some text notes about parent object
-
-
- .. py:attribute:: color
-
- string (*value field*) A string to hold a text string specifying display color.Can be a regular English color name, or an rgb code rrrgggbbb
-
-
- .. py:attribute:: textColor
-
- string (*value field*) A string to hold a text string specifying color for text labelthat might be on the display for this object.Can be a regular English color name, or an rgb code rrrgggbbb
-
-
- .. py:attribute:: icon
-
- string (*value field*) A string to specify icon to use for display
-
-
-.. py:class:: Arith
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setFunction
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getFunction
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setOutputValue
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getOutputValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getArg1Value
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setAnyValue
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getAnyValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: arg1
-
- (*destination message field*) Handles argument 1. This just assigns it
-
-
- .. py:method:: arg2
-
- (*destination message field*) Handles argument 2. This just assigns it
-
-
- .. py:method:: arg3
-
- (*destination message field*) Handles argument 3. This sums in each input, and clears each clock tick.
-
-
- .. py:method:: arg1x2
-
- (*destination message field*) Store the product of the two arguments in output\_
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: output
-
- double (*source message field*) Sends out the computed value
-
-
- .. py:attribute:: function
-
- string (*value field*) Arithmetic function to perform on inputs.
-
-
- .. py:attribute:: outputValue
-
- double (*value field*) Value of output as computed last timestep.
-
-
- .. py:attribute:: arg1Value
-
- double (*value field*) Value of arg1 as computed last timestep.
-
-
- .. py:attribute:: anyValue
-
- unsigned int,double (*lookup field*) Value of any of the internal fields, output, arg1, arg2, arg3,as specified by the index argument from 0 to 3.
-
-
-.. py:class:: BufPool
-
-
-.. py:class:: CaConc
-
- CaConc: Calcium concentration pool. Takes current from a channel and keeps track of calcium buildup and depletion by a single exponential process.
-
-.. py:class:: CaConcBase
-
- CaConcBase: Base class for Calcium concentration pool. Takes current from a channel and keeps track of calcium buildup and depletion by a single exponential process.
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message to receive Process message from scheduler
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: setCa
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCa
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCaBasal
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCaBasal
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCa_base
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCa_base
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTau
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTau
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setThick
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThick
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCeiling
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCeiling
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setFloor
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getFloor
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: current
-
- (*destination message field*) Calcium Ion current, due to be converted to conc.
-
-
- .. py:method:: currentFraction
-
- (*destination message field*) Fraction of total Ion current, that is carried by Ca2+.
-
-
- .. py:method:: increase
-
- (*destination message field*) Any input current that increases the concentration.
-
-
- .. py:method:: decrease
-
- (*destination message field*) Any input current that decreases the concentration.
-
-
- .. py:method:: basal
-
- (*destination message field*) Synonym for assignment of basal conc.
-
-
- .. py:attribute:: concOut
-
- double (*source message field*) Concentration of Ca in pool
-
-
- .. py:attribute:: Ca
-
- double (*value field*) Calcium concentration.
-
-
- .. py:attribute:: CaBasal
-
- double (*value field*) Basal Calcium concentration.
-
-
- .. py:attribute:: Ca_base
-
- double (*value field*) Basal Calcium concentration, synonym for CaBasal
-
-
- .. py:attribute:: tau
-
- double (*value field*) Settling time for Ca concentration
-
-
- .. py:attribute:: B
-
- double (*value field*) Volume scaling factor
-
-
- .. py:attribute:: thick
-
- double (*value field*) Thickness of Ca shell.
-
-
- .. py:attribute:: ceiling
-
- double (*value field*) Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.
-
-
- .. py:attribute:: floor
-
- double (*value field*) Floor value for Ca concentration. If Ca < floor, Ca = floor
-
-
-.. py:class:: ChanBase
-
- ChanBase: Base class for assorted ion channels.Presents a common interface for all of them.
-
- .. py:attribute:: channel
-
- void (*shared message field*) This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
-
-
- .. py:attribute:: ghk
-
- void (*shared message field*) Message to Goldman-Hodgkin-Katz object
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message to receive Process message from scheduler
-
-
- .. py:method:: Vm
-
- (*destination message field*) Handles Vm message coming in from compartment
-
-
- .. py:method:: Vm
-
- (*destination message field*) Handles Vm message coming in from compartment
-
-
- .. py:method:: setGbar
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getGbar
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setEk
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getEk
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setGk
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getGk
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getIk
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: channelOut
-
- double,double (*source message field*) Sends channel variables Gk and Ek to compartment
-
-
- .. py:attribute:: permeabilityOut
-
- double (*source message field*) Conductance term going out to GHK object
-
-
- .. py:attribute:: IkOut
-
- double (*source message field*) Channel current. This message typically goes to concenobjects that keep track of ion concentration.
-
-
- .. py:attribute:: Gbar
-
- double (*value field*) Maximal channel conductance
-
-
- .. py:attribute:: Ek
-
- double (*value field*) Reversal potential of channel
-
-
- .. py:attribute:: Gk
-
- double (*value field*) Channel conductance variable
-
-
- .. py:attribute:: Ik
-
- double (*value field*) Channel current variable
-
-
-.. py:class:: ChemCompt
-
- Pure virtual base class for chemical compartments
-
- .. py:method:: setVolume
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVolume
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getVoxelVolume
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getVoxelMidpoint
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getOneVoxelVolume
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumDimensions
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getStencilRate
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getStencilIndex
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: buildDefaultMesh
-
- (*destination message field*) Tells ChemCompt derived class to build a default mesh with thespecified volume and number of meshEntries.
-
-
- .. py:method:: setVolumeNotRates
-
- (*destination message field*) Changes volume but does not notify any child objects.Only works if the ChemCompt has just one voxel.This function will invalidate any concentration term inthe model. If you don't know why you would want to do this,then you shouldn't use this function.
-
-
- .. py:method:: resetStencil
-
- (*destination message field*) Resets the diffusion stencil to the core stencil that only includes the within-mesh diffusion. This is needed prior to building up the cross-mesh diffusion through junctions.
-
-
- .. py:method:: setNumMesh
-
- (*destination message field*) Assigns number of field entries in field array.
-
-
- .. py:method:: getNumMesh
-
- (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: voxelVolOut
-
- vector<double> (*source message field*) Sends updated voxel volume out to Ksolve, Gsolve, and Dsolve.Used to request a recalculation of rates and of initial numbers.
-
-
- .. py:attribute:: volume
-
- double (*value field*) Volume of entire chemical domain.Assigning this only works if the chemical compartment hasonly a single voxel. Otherwise ignored.This function goes through all objects below this on thetree, and rescales their molecule #s and rates as per thevolume change. This keeps concentration the same, and alsomaintains rates as expressed in volume units.
-
-
- .. py:attribute:: voxelVolume
-
- vector<double> (*value field*) Vector of volumes of each of the voxels.
-
-
- .. py:attribute:: voxelMidpoint
-
- vector<double> (*value field*) Vector of midpoint coordinates of each of the voxels. The size of this vector is 3N, where N is the number of voxels. The first N entries are for x, next N for y, last N are z.
-
-
- .. py:attribute:: numDimensions
-
- unsigned int (*value field*) Number of spatial dimensions of this compartment. Usually 3 or 2
-
-
- .. py:attribute:: oneVoxelVolume
-
- unsigned int,double (*lookup field*) Volume of specified voxel.
-
-
- .. py:attribute:: stencilRate
-
- unsigned int,vector<double> (*lookup field*) vector of diffusion rates in the stencil for specified voxel.The identity of the coupled voxels is given by the partner field 'stencilIndex'.Returns an empty vector for non-voxelized compartments.
-
-
- .. py:attribute:: stencilIndex
-
- unsigned int,vector<unsigned int> (*lookup field*) vector of voxels diffusively coupled to the specified voxel.The diffusion rates into the coupled voxels is given by the partner field 'stencilRate'.Returns an empty vector for non-voxelized compartments.
-
-
-.. py:class:: Cinfo
-
- Class information object.
-
- .. py:method:: getDocs
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getBaseClass
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: docs
-
- string (*value field*) Documentation
-
-
- .. py:attribute:: baseClass
-
- string (*value field*) Name of base class
-
-
-.. py:class:: Clock
-
- Clock: Clock class. Handles sequencing of operations in simulations.Every object scheduled for operations in MOOSE is connected to oneof the 'Tick' entries on the Clock.
- The Clock manages 32 'Ticks', each of which has its own dt,which is an integral multiple of the clock baseDt\_. On every clock step the ticks are examined to see which of themis due for updating. When a tick is updated, the 'process' call of all the objects scheduled on that tick is called. Order of execution: If a subset of ticks are scheduled for execution at a given timestep, then they will be executed in numerical order, lowest tick first and highest last. There is no guarantee of execution order for objects within a clock tick.
- The clock provides default scheduling for all objects which can be accessed using Clock::lookupDefaultTick( className ). Specific items of note are that the output/file dump objects are second-last, and the postmaster is last on the order of Ticks. The clock also starts up with some default timesteps for each of these ticks, and this can be overridden using the shell command setClock, or by directly assigning tickStep values on the clock object.
- Which objects use which tick? As a rule of thumb, try this:
- Electrical/compartmental model calculations: Ticks 0-7
- Tables and output objects for electrical output: Tick 8
- Diffusion solver: Tick 10
- Chemical/compartmental model calculations: Ticks 11-17
- Tables and output objects for chemical output: Tick 18
- Unassigned: Ticks 20-29
- Special: 30-31
- Data output is a bit special, since you may want to store data at different rates for electrical and chemical processes in the same model. Here you will have to specifically assign distinct clock ticks for the tables/fileIO objects handling output at different time-resolutions. Typically one uses tick 8 and 18.
- Here are the detailed mappings of class to tick.
- Class Tick dt
- DiffAmp 0 50e-6
- Interpol 0 50e-6
- PIDController 0 50e-6
- PulseGen 0 50e-6
- StimulusTable 0 50e-6
- testSched 0 50e-6
- VClamp 0 50e-6
- SynHandlerBase 1 50e-6
- SimpleSynHandler 1 50e-6
- CaConc 1 50e-6
- CaConcBase 1 50e-6
- DifShell 1 50e-6
- MgBlock 1 50e-6
- Nernst 1 50e-6
- RandSpike 1 50e-6
- ChanBase 2 50e-6
- IntFire 2 50e-6
- IntFireBase 2 50e-6
- LIF 2 50e-6
- IzhikevichNrn 2 50e-6
- SynChan 2 50e-6
- GapJunction 2 50e-6
- HHChannel 2 50e-6
- HHChannel2D 2 50e-6
- Leakage 2 50e-6
- MarkovChannel 2 50e-6
- MarkovGslSolver 2 50e-6
- MarkovRateTable 2 50e-6
- MarkovSolver 2 50e-6
- MarkovSolverBase 2 50e-6
- RC 2 50e-6
- Compartment (init) 3 50e-6
- CompartmentBase (init ) 3 50e-6
- SymCompartment (init) 3 50e-6
- Compartment 4 50e-6
- CompartmentBase 4 50e-6
- SymCompartment 4 50e-6
- SpikeGen 5 50e-6
- HSolve 6 50e-6
- SpikeStats 7 50e-6
- Dsolve 10 0.01
- Adaptor 11 0.1
- Func 12 0.1
- Function 12 0.1
- Arith 12 0.1
- FuncBase 12 0.1
- FuncPool 12 0.1
- MathFunc 12 0.1
- SumFunc 12 0.1
- BufPool 13 0.1
- Pool 13 0.1
- PoolBase 13 0.1
- CplxEnzBase 14 0.1
- Enz 14 0.1
- EnzBase 14 0.1
- MMenz 14 0.1
- Reac 14 0.1
- ReacBase 14 0.1
- Gsolve (init) 15 0.1
- Ksolve (init) 15 0.1
- Gsolve 16 0.1
- Ksolve 16 0.1
- Stats 17 1
- Table 18 1
- TimeTable 18 1
- HDF5DataWriter 30 1
- HDF5WriterBase 30 1
- PostMaster 31 0.01
-
- Note that the other classes are not scheduled at all.
-
- .. py:attribute:: clockControl
-
- void (*shared message field*) Controls all scheduling aspects of Clock, usually from Shell
-
-
- .. py:attribute:: proc0
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc1
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc2
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc3
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc4
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc5
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc6
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc7
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc8
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc9
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc10
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc11
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc12
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc13
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc14
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc15
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc16
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc17
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc18
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc19
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc20
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc21
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc22
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc23
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc24
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc25
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc26
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc27
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc28
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc29
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc30
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:attribute:: proc31
-
- void (*shared message field*) Shared process/reinit message
-
-
- .. py:method:: setBaseDt
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getBaseDt
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getRunTime
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getCurrentTime
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNsteps
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumTicks
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getCurrentStep
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDts
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getIsRunning
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTickStep
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTickStep
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTickDt
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTickDt
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: start
-
- (*destination message field*) Sets off the simulation for the specified duration
-
-
- .. py:method:: step
-
- (*destination message field*) Sets off the simulation for the specified # of steps
-
-
- .. py:method:: stop
-
- (*destination message field*) Halts the simulation, with option to restart seamlessly
-
-
- .. py:method:: reinit
-
- (*destination message field*) Zeroes out all ticks, starts at t = 0
-
-
- .. py:attribute:: finished
-
- void (*source message field*) Signal for completion of run
-
-
- .. py:attribute:: process0
-
- PK8ProcInfo (*source message field*) process for Tick 0
-
-
- .. py:attribute:: reinit0
-
- PK8ProcInfo (*source message field*) reinit for Tick 0
-
-
- .. py:attribute:: process1
-
- PK8ProcInfo (*source message field*) process for Tick 1
-
-
- .. py:attribute:: reinit1
-
- PK8ProcInfo (*source message field*) reinit for Tick 1
-
-
- .. py:attribute:: process2
-
- PK8ProcInfo (*source message field*) process for Tick 2
-
-
- .. py:attribute:: reinit2
-
- PK8ProcInfo (*source message field*) reinit for Tick 2
-
-
- .. py:attribute:: process3
-
- PK8ProcInfo (*source message field*) process for Tick 3
-
-
- .. py:attribute:: reinit3
-
- PK8ProcInfo (*source message field*) reinit for Tick 3
-
-
- .. py:attribute:: process4
-
- PK8ProcInfo (*source message field*) process for Tick 4
-
-
- .. py:attribute:: reinit4
-
- PK8ProcInfo (*source message field*) reinit for Tick 4
-
-
- .. py:attribute:: process5
-
- PK8ProcInfo (*source message field*) process for Tick 5
-
-
- .. py:attribute:: reinit5
-
- PK8ProcInfo (*source message field*) reinit for Tick 5
-
-
- .. py:attribute:: process6
-
- PK8ProcInfo (*source message field*) process for Tick 6
-
-
- .. py:attribute:: reinit6
-
- PK8ProcInfo (*source message field*) reinit for Tick 6
-
-
- .. py:attribute:: process7
-
- PK8ProcInfo (*source message field*) process for Tick 7
-
-
- .. py:attribute:: reinit7
-
- PK8ProcInfo (*source message field*) reinit for Tick 7
-
-
- .. py:attribute:: process8
-
- PK8ProcInfo (*source message field*) process for Tick 8
-
-
- .. py:attribute:: reinit8
-
- PK8ProcInfo (*source message field*) reinit for Tick 8
-
-
- .. py:attribute:: process9
-
- PK8ProcInfo (*source message field*) process for Tick 9
-
-
- .. py:attribute:: reinit9
-
- PK8ProcInfo (*source message field*) reinit for Tick 9
-
-
- .. py:attribute:: process10
-
- PK8ProcInfo (*source message field*) process for Tick 10
-
-
- .. py:attribute:: reinit10
-
- PK8ProcInfo (*source message field*) reinit for Tick 10
-
-
- .. py:attribute:: process11
-
- PK8ProcInfo (*source message field*) process for Tick 11
-
-
- .. py:attribute:: reinit11
-
- PK8ProcInfo (*source message field*) reinit for Tick 11
-
-
- .. py:attribute:: process12
-
- PK8ProcInfo (*source message field*) process for Tick 12
-
-
- .. py:attribute:: reinit12
-
- PK8ProcInfo (*source message field*) reinit for Tick 12
-
-
- .. py:attribute:: process13
-
- PK8ProcInfo (*source message field*) process for Tick 13
-
-
- .. py:attribute:: reinit13
-
- PK8ProcInfo (*source message field*) reinit for Tick 13
-
-
- .. py:attribute:: process14
-
- PK8ProcInfo (*source message field*) process for Tick 14
-
-
- .. py:attribute:: reinit14
-
- PK8ProcInfo (*source message field*) reinit for Tick 14
-
-
- .. py:attribute:: process15
-
- PK8ProcInfo (*source message field*) process for Tick 15
-
-
- .. py:attribute:: reinit15
-
- PK8ProcInfo (*source message field*) reinit for Tick 15
-
-
- .. py:attribute:: process16
-
- PK8ProcInfo (*source message field*) process for Tick 16
-
-
- .. py:attribute:: reinit16
-
- PK8ProcInfo (*source message field*) reinit for Tick 16
-
-
- .. py:attribute:: process17
-
- PK8ProcInfo (*source message field*) process for Tick 17
-
-
- .. py:attribute:: reinit17
-
- PK8ProcInfo (*source message field*) reinit for Tick 17
-
-
- .. py:attribute:: process18
-
- PK8ProcInfo (*source message field*) process for Tick 18
-
-
- .. py:attribute:: reinit18
-
- PK8ProcInfo (*source message field*) reinit for Tick 18
-
-
- .. py:attribute:: process19
-
- PK8ProcInfo (*source message field*) process for Tick 19
-
-
- .. py:attribute:: reinit19
-
- PK8ProcInfo (*source message field*) reinit for Tick 19
-
-
- .. py:attribute:: process20
-
- PK8ProcInfo (*source message field*) process for Tick 20
-
-
- .. py:attribute:: reinit20
-
- PK8ProcInfo (*source message field*) reinit for Tick 20
-
-
- .. py:attribute:: process21
-
- PK8ProcInfo (*source message field*) process for Tick 21
-
-
- .. py:attribute:: reinit21
-
- PK8ProcInfo (*source message field*) reinit for Tick 21
-
-
- .. py:attribute:: process22
-
- PK8ProcInfo (*source message field*) process for Tick 22
-
-
- .. py:attribute:: reinit22
-
- PK8ProcInfo (*source message field*) reinit for Tick 22
-
-
- .. py:attribute:: process23
-
- PK8ProcInfo (*source message field*) process for Tick 23
-
-
- .. py:attribute:: reinit23
-
- PK8ProcInfo (*source message field*) reinit for Tick 23
-
-
- .. py:attribute:: process24
-
- PK8ProcInfo (*source message field*) process for Tick 24
-
-
- .. py:attribute:: reinit24
-
- PK8ProcInfo (*source message field*) reinit for Tick 24
-
-
- .. py:attribute:: process25
-
- PK8ProcInfo (*source message field*) process for Tick 25
-
-
- .. py:attribute:: reinit25
-
- PK8ProcInfo (*source message field*) reinit for Tick 25
-
-
- .. py:attribute:: process26
-
- PK8ProcInfo (*source message field*) process for Tick 26
-
-
- .. py:attribute:: reinit26
-
- PK8ProcInfo (*source message field*) reinit for Tick 26
-
-
- .. py:attribute:: process27
-
- PK8ProcInfo (*source message field*) process for Tick 27
-
-
- .. py:attribute:: reinit27
-
- PK8ProcInfo (*source message field*) reinit for Tick 27
-
-
- .. py:attribute:: process28
-
- PK8ProcInfo (*source message field*) process for Tick 28
-
-
- .. py:attribute:: reinit28
-
- PK8ProcInfo (*source message field*) reinit for Tick 28
-
-
- .. py:attribute:: process29
-
- PK8ProcInfo (*source message field*) process for Tick 29
-
-
- .. py:attribute:: reinit29
-
- PK8ProcInfo (*source message field*) reinit for Tick 29
-
-
- .. py:attribute:: process30
-
- PK8ProcInfo (*source message field*) process for Tick 30
-
-
- .. py:attribute:: reinit30
-
- PK8ProcInfo (*source message field*) reinit for Tick 30
-
-
- .. py:attribute:: process31
-
- PK8ProcInfo (*source message field*) process for Tick 31
-
-
- .. py:attribute:: reinit31
-
- PK8ProcInfo (*source message field*) reinit for Tick 31
-
-
- .. py:attribute:: baseDt
-
- double (*value field*) Base timestep for simulation. This is the smallest dt out of all the clock ticks. By definition all other timesteps are integral multiples of this, and are rounded to ensure that this is the case .
-
-
- .. py:attribute:: runTime
-
- double (*value field*) Duration to run the simulation
-
-
- .. py:attribute:: currentTime
-
- double (*value field*) Current simulation time
-
-
- .. py:attribute:: nsteps
-
- unsigned int (*value field*) Number of steps to advance the simulation, in units of the smallest timestep on the clock ticks
-
-
- .. py:attribute:: numTicks
-
- unsigned int (*value field*) Number of clock ticks
-
-
- .. py:attribute:: currentStep
-
- unsigned int (*value field*) Current simulation step
-
-
- .. py:attribute:: dts
-
- vector<double> (*value field*) Utility function returning the dt (timestep) of all ticks.
-
-
- .. py:attribute:: isRunning
-
- bool (*value field*) Utility function to report if simulation is in progress.
-
-
- .. py:attribute:: tickStep
-
- unsigned int,unsigned int (*lookup field*) Step size of specified Tick, as integral multiple of dt\_ A zero step size means that the Tick is inactive
-
-
- .. py:attribute:: tickDt
-
- unsigned int,double (*lookup field*) Timestep dt of specified Tick. Always integral multiple of dt\_. If you assign a non-integer multiple it will round off. A zero timestep means that the Tick is inactive
-
-
-.. py:class:: Compartment
-
- Compartment object, for branching neuron models.
-
-.. py:class:: CompartmentBase
-
- CompartmentBase object, for branching neuron models.
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process messages from the scheduler objects. The Process should be called `second` in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:attribute:: init
-
- void (*shared message field*) This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:attribute:: channel
-
- void (*shared message field*) This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm
-
-
- .. py:attribute:: axial
-
- void (*shared message field*) This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.
-
-
- .. py:attribute:: raxial
-
- void (*shared message field*) This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.
-
-
- .. py:method:: setVm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setEm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getEm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getIm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInject
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInject
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInitVm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInitVm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRa
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRa
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDiameter
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDiameter
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setLength
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLength
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setX0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setX
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: injectMsg
-
- (*destination message field*) The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
-
-
- .. py:method:: randInject
-
- (*destination message field*) Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.
-
-
- .. py:method:: injectMsg
-
- (*destination message field*) The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
-
-
- .. py:method:: cable
-
- (*destination message field*) Message for organizing compartments into groups, calledcables. Doesn't do anything.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles 'process' call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles 'reinit' call
-
-
- .. py:method:: initProc
-
- (*destination message field*) Handles Process call for the 'init' phase of the CompartmentBase calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.
-
-
- .. py:method:: initReinit
-
- (*destination message field*) Handles Reinit call for the 'init' phase of the CompartmentBase calculations.
-
-
- .. py:method:: handleChannel
-
- (*destination message field*) Handles conductance and Reversal potential arguments from Channel
-
-
- .. py:method:: handleRaxial
-
- (*destination message field*) Handles Raxial info: arguments are Ra and Vm.
-
-
- .. py:method:: handleAxial
-
- (*destination message field*) Handles Axial information. Argument is just Vm.
-
-
- .. py:attribute:: VmOut
-
- double (*source message field*) Sends out Vm value of compartment on each timestep
-
-
- .. py:attribute:: axialOut
-
- double (*source message field*) Sends out Vm value of compartment to adjacent compartments,on each timestep
-
-
- .. py:attribute:: raxialOut
-
- double,double (*source message field*) Sends out Raxial information on each timestep, fields are Ra and Vm
-
-
- .. py:attribute:: Vm
-
- double (*value field*) membrane potential
-
-
- .. py:attribute:: Cm
-
- double (*value field*) Membrane capacitance
-
-
- .. py:attribute:: Em
-
- double (*value field*) Resting membrane potential
-
-
- .. py:attribute:: Im
-
- double (*value field*) Current going through membrane
-
-
- .. py:attribute:: inject
-
- double (*value field*) Current injection to deliver into compartment
-
-
- .. py:attribute:: initVm
-
- double (*value field*) Initial value for membrane potential
-
-
- .. py:attribute:: Rm
-
- double (*value field*) Membrane resistance
-
-
- .. py:attribute:: Ra
-
- double (*value field*) Axial resistance of compartment
-
-
- .. py:attribute:: diameter
-
- double (*value field*) Diameter of compartment
-
-
- .. py:attribute:: length
-
- double (*value field*) Length of compartment
-
-
- .. py:attribute:: x0
-
- double (*value field*) X coordinate of start of compartment
-
-
- .. py:attribute:: y0
-
- double (*value field*) Y coordinate of start of compartment
-
-
- .. py:attribute:: z0
-
- double (*value field*) Z coordinate of start of compartment
-
-
- .. py:attribute:: x
-
- double (*value field*) x coordinate of end of compartment
-
-
- .. py:attribute:: y
-
- double (*value field*) y coordinate of end of compartment
-
-
- .. py:attribute:: z
-
- double (*value field*) z coordinate of end of compartment
-
-
-.. py:class:: CplxEnzBase
-
- : Base class for mass-action enzymes in which there is an explicit pool for the enzyme-substrate complex. It models the reaction: E + S <===> E.S ----> E + P
-
- .. py:attribute:: enz
-
- void (*shared message field*) Connects to enzyme pool
-
-
- .. py:attribute:: cplx
-
- void (*shared message field*) Connects to enz-sub complex pool
-
-
- .. py:method:: setK1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getK1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setK2
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getK2
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setK3
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getK3
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRatio
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRatio
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setConcK1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getConcK1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: enzDest
-
- (*destination message field*) Handles # of molecules of Enzyme
-
-
- .. py:method:: cplxDest
-
- (*destination message field*) Handles # of molecules of enz-sub complex
-
-
- .. py:attribute:: enzOut
-
- double,double (*source message field*) Sends out increment of molecules on product each timestep
-
-
- .. py:attribute:: cplxOut
-
- double,double (*source message field*) Sends out increment of molecules on product each timestep
-
-
- .. py:attribute:: k1
-
- double (*value field*) Forward reaction from enz + sub to complex, in # units.This parameter is subordinate to the Km. This means thatwhen Km is changed, this changes. It also means that whenk2 or k3 (aka kcat) are changed, we assume that Km remainsfixed, and as a result k1 must change. It is only whenk1 is assigned directly that we assume that the user knowswhat they are doing, and we adjust Km accordingly.k1 is also subordinate to the 'ratio' field, since setting the ratio reassigns k2.Should you wish to assign the elementary rates k1, k2, k3,of an enzyme directly, always assign k1 last.
-
-
- .. py:attribute:: k2
-
- double (*value field*) Reverse reaction from complex to enz + sub
-
-
- .. py:attribute:: k3
-
- double (*value field*) Forward rate constant from complex to product + enz
-
-
- .. py:attribute:: ratio
-
- double (*value field*) Ratio of k2/k3
-
-
- .. py:attribute:: concK1
-
- double (*value field*) K1 expressed in concentration (1/millimolar.sec) unitsThis parameter is subordinate to the Km. This means thatwhen Km is changed, this changes. It also means that whenk2 or k3 (aka kcat) are changed, we assume that Km remainsfixed, and as a result concK1 must change. It is only whenconcK1 is assigned directly that we assume that the user knowswhat they are doing, and we adjust Km accordingly.concK1 is also subordinate to the 'ratio' field, sincesetting the ratio reassigns k2.Should you wish to assign the elementary rates concK1, k2, k3,of an enzyme directly, always assign concK1 last.
-
-
-.. py:class:: CubeMesh
-
-
- .. py:method:: setIsToroid
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getIsToroid
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setPreserveNumEntries
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getPreserveNumEntries
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setAlwaysDiffuse
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getAlwaysDiffuse
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setX0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setX1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDx
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDx
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDy
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDy
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDz
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDz
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNx
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNx
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNy
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNy
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNz
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNz
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCoords
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCoords
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMeshToSpace
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMeshToSpace
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSpaceToMesh
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSpaceToMesh
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSurface
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSurface
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: isToroid
-
- bool (*value field*) Flag. True when the mesh should be toroidal, that is,when going beyond the right face brings us around to theleft-most mesh entry, and so on. If we have nx, ny, nzentries, this rule means that the coordinate (x, ny, z)will map onto (x, 0, z). Similarly,(-1, y, z) -> (nx-1, y, z)Default is false
-
-
- .. py:attribute:: preserveNumEntries
-
- bool (*value field*) Flag. When it is true, the numbers nx, ny, nz remainunchanged when x0, x1, y0, y1, z0, z1 are altered. Thusdx, dy, dz would change instead. When it is false, thendx, dy, dz remain the same and nx, ny, nz are altered.Default is true
-
-
- .. py:attribute:: alwaysDiffuse
-
- bool (*value field*) Flag. When it is true, the mesh matches up sequential mesh entries for diffusion and chmestry. This is regardless of spatial location, and is guaranteed to set up at least the home reaction systemDefault is false
-
-
- .. py:attribute:: x0
-
- double (*value field*) X coord of one end
-
-
- .. py:attribute:: y0
-
- double (*value field*) Y coord of one end
-
-
- .. py:attribute:: z0
-
- double (*value field*) Z coord of one end
-
-
- .. py:attribute:: x1
-
- double (*value field*) X coord of other end
-
-
- .. py:attribute:: y1
-
- double (*value field*) Y coord of other end
-
-
- .. py:attribute:: z1
-
- double (*value field*) Z coord of other end
-
-
- .. py:attribute:: dx
-
- double (*value field*) X size for mesh
-
-
- .. py:attribute:: dy
-
- double (*value field*) Y size for mesh
-
-
- .. py:attribute:: dz
-
- double (*value field*) Z size for mesh
-
-
- .. py:attribute:: nx
-
- unsigned int (*value field*) Number of subdivisions in mesh in X
-
-
- .. py:attribute:: ny
-
- unsigned int (*value field*) Number of subdivisions in mesh in Y
-
-
- .. py:attribute:: nz
-
- unsigned int (*value field*) Number of subdivisions in mesh in Z
-
-
- .. py:attribute:: coords
-
- vector<double> (*value field*) Set all the coords of the cuboid at once. Order is:x0 y0 z0 x1 y1 z1 dx dy dzWhen this is done, it recalculates the numEntries since dx, dy and dz are given explicitly.As a special hack, you can leave out dx, dy and dz and use a vector of size 6. In this case the operation assumes that nx, ny and nz are to be preserved and dx, dy and dz will be recalculated.
-
-
- .. py:attribute:: meshToSpace
-
- vector<unsigned int> (*value field*) Array in which each mesh entry stores spatial (cubic) index
-
-
- .. py:attribute:: spaceToMesh
-
- vector<unsigned int> (*value field*) Array in which each space index (obtained by linearizing the xyz coords) specifies which meshIndex is present.In many cases the index will store the EMPTY flag if there isno mesh entry at that spatial location
-
-
- .. py:attribute:: surface
-
- vector<unsigned int> (*value field*) Array specifying surface of arbitrary volume within the CubeMesh. All entries must fall within the cuboid. Each entry of the array is a spatial index obtained by linearizing the ix, iy, iz coordinates within the cuboid. So, each entry == ( iz * ny + iy ) * nx + ixNote that the voxels listed on the surface are WITHIN the volume of the CubeMesh object
-
-
-.. py:class:: CylMesh
-
-
- .. py:method:: setX0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setR0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getR0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setX1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setR1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getR1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDiffLength
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDiffLength
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCoords
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCoords
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumDiffCompts
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getTotLength
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: x0
-
- double (*value field*) x coord of one end
-
-
- .. py:attribute:: y0
-
- double (*value field*) y coord of one end
-
-
- .. py:attribute:: z0
-
- double (*value field*) z coord of one end
-
-
- .. py:attribute:: r0
-
- double (*value field*) Radius of one end
-
-
- .. py:attribute:: x1
-
- double (*value field*) x coord of other end
-
-
- .. py:attribute:: y1
-
- double (*value field*) y coord of other end
-
-
- .. py:attribute:: z1
-
- double (*value field*) z coord of other end
-
-
- .. py:attribute:: r1
-
- double (*value field*) Radius of other end
-
-
- .. py:attribute:: diffLength
-
- double (*value field*) Length constant to use for subdivisionsThe system will attempt to subdivide using compartments oflength diffLength on average. If the cylinder has different enddiameters r0 and r1, it will scale to smaller lengthsfor the smaller diameter end and vice versa.Once the value is set it will recompute diffLength as totLength/numEntries
-
-
- .. py:attribute:: coords
-
- vector<double> (*value field*) All the coords as a single vector: x0 y0 z0 x1 y1 z1 r0 r1 diffLength
-
-
- .. py:attribute:: numDiffCompts
-
- unsigned int (*value field*) Number of diffusive compartments in model
-
-
- .. py:attribute:: totLength
-
- double (*value field*) Total length of cylinder
-
-
-.. py:class:: DiagonalMsg
-
-
- .. py:method:: setStride
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStride
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: stride
-
- int (*value field*) The stride is the increment to the src DataId that gives thedest DataId. It can be positive or negative, but bounds checkingtakes place and it does not wrap around.
-
-
-.. py:class:: DifShell
-
- DifShell object: Models diffusion of an ion (typically calcium) within an electric compartment. A DifShell is an iso-concentration region with respect to the ion. Adjoining DifShells exchange flux of this ion, and also keep track of changes in concentration due to pumping, buffering and channel currents, by talking to the appropriate objects.
-
- .. py:attribute:: process_0
-
- void (*shared message field*) Here we create 2 shared finfos to attach with the Ticks. This is because we want to perform DifShell computations in 2 stages, much as in the Compartment object. In the first stage we send out the concentration value to other DifShells and Buffer elements. We also receive fluxes and currents and sum them up to compute ( dC / dt ). In the second stage we find the new C value using an explicit integration method. This 2-stage procedure eliminates the need to store and send prev\_C values, as was common in GENESIS.
-
-
- .. py:attribute:: process_1
-
- void (*shared message field*) Second process call
-
-
- .. py:attribute:: buffer
-
- void (*shared message field*) This is a shared message from a DifShell to a Buffer (FixBuffer or DifBuffer). During stage 0::
-
- * DifShell sends ion concentration
- * Buffer updates buffer concentration and sends it back immediately using a call-back.
- * DifShell updates the time-derivative ( dC / dt )
-
- During stage 1:
- * DifShell advances concentration C
-
- This scheme means that the Buffer does not need to be scheduled, and it does its computations when it receives a cue from the DifShell. May not be the best idea, but it saves us from doing the above computations in 3 stages instead of 2.
-
-
- .. py:attribute:: innerDif
-
- void (*shared message field*) This shared message (and the next) is between DifShells: adjoining shells exchange information to find out the flux between them. Using this message, an inner shell sends to, and receives from its outer shell.
-
-
- .. py:attribute:: outerDif
-
- void (*shared message field*) Using this message, an outer shell sends to, and receives from its inner shell.
-
-
- .. py:method:: getC
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCeq
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCeq
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setD
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getD
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setValence
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getValence
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setLeak
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLeak
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setShapeMode
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getShapeMode
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setLength
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLength
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDiameter
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDiameter
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setThickness
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThickness
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setVolume
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVolume
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setOuterArea
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getOuterArea
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInnerArea
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInnerArea
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Reinit happens only in stage 0
-
-
- .. py:method:: process
-
- (*destination message field*) Handle process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Reinit happens only in stage 0
-
-
- .. py:method:: reaction
-
- (*destination message field*) Here the DifShell receives reaction rates (forward and backward), and concentrations for the free-buffer and bound-buffer molecules.
-
-
- .. py:method:: fluxFromOut
-
- (*destination message field*) Destination message
-
-
- .. py:method:: fluxFromIn
-
- (*destination message field*)
-
-
- .. py:method:: influx
-
- (*destination message field*)
-
-
- .. py:method:: outflux
-
- (*destination message field*)
-
-
- .. py:method:: fInflux
-
- (*destination message field*)
-
-
- .. py:method:: fOutflux
-
- (*destination message field*)
-
-
- .. py:method:: storeInflux
-
- (*destination message field*)
-
-
- .. py:method:: storeOutflux
-
- (*destination message field*)
-
-
- .. py:method:: tauPump
-
- (*destination message field*)
-
-
- .. py:method:: eqTauPump
-
- (*destination message field*)
-
-
- .. py:method:: mmPump
-
- (*destination message field*)
-
-
- .. py:method:: hillPump
-
- (*destination message field*)
-
-
- .. py:attribute:: concentrationOut
-
- double (*source message field*) Sends out concentration
-
-
- .. py:attribute:: innerDifSourceOut
-
- double,double (*source message field*) Sends out source information.
-
-
- .. py:attribute:: outerDifSourceOut
-
- double,double (*source message field*) Sends out source information.
-
-
- .. py:attribute:: C
-
- double (*value field*) Concentration C is computed by the DifShell and is read-only
-
-
- .. py:attribute:: Ceq
-
- double (*value field*)
-
-
- .. py:attribute:: D
-
- double (*value field*)
-
-
- .. py:attribute:: valence
-
- double (*value field*)
-
-
- .. py:attribute:: leak
-
- double (*value field*)
-
-
- .. py:attribute:: shapeMode
-
- unsigned int (*value field*)
-
-
- .. py:attribute:: length
-
- double (*value field*)
-
-
- .. py:attribute:: diameter
-
- double (*value field*)
-
-
- .. py:attribute:: thickness
-
- double (*value field*)
-
-
- .. py:attribute:: volume
-
- double (*value field*)
-
-
- .. py:attribute:: outerArea
-
- double (*value field*)
-
-
- .. py:attribute:: innerArea
-
- double (*value field*)
-
-
-.. py:class:: DiffAmp
-
- A difference amplifier. Output is the difference between the total plus inputs and the total minus inputs multiplied by gain. Gain can be set statically as a field or can be a destination message and thus dynamically determined by the output of another object. Same as GENESIS diffamp object.
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: setGain
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getGain
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSaturation
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSaturation
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getOutputValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: gainIn
-
- (*destination message field*) Destination message to control gain dynamically.
-
-
- .. py:method:: plusIn
-
- (*destination message field*) Positive input terminal of the amplifier. All the messages connected here are summed up to get total positive input.
-
-
- .. py:method:: minusIn
-
- (*destination message field*) Negative input terminal of the amplifier. All the messages connected here are summed up to get total positive input.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call, updates internal time stamp.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call.
-
-
- .. py:attribute:: output
-
- double (*source message field*) Current output level.
-
-
- .. py:attribute:: gain
-
- double (*value field*) Gain of the amplifier. The output of the amplifier is the difference between the totals in plus and minus inputs multiplied by the gain. Defaults to 1
-
-
- .. py:attribute:: saturation
-
- double (*value field*) Saturation is the bound on the output. If output goes beyond the +/-saturation range, it is truncated to the closer of +saturation and -saturation. Defaults to the maximum double precision floating point number representable on the system.
-
-
- .. py:attribute:: outputValue
-
- double (*value field*) Output of the amplifier, i.e. gain * (plus - minus).
-
-
-.. py:class:: Dsolve
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setStoich
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStoich
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setPath
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getPath
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCompartment
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCompartment
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumVoxels
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumAllVoxels
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNVec
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNVec
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumPools
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumPools
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: buildNeuroMeshJunctions
-
- (*destination message field*) Builds junctions between NeuroMesh, SpineMesh and PsdMesh
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: stoich
-
- Id (*value field*) Stoichiometry object for handling this reaction system.
-
-
- .. py:attribute:: path
-
- string (*value field*) Path of reaction system. Must include all the pools that are to be handled by the Dsolve, can also include other random objects, which will be ignored.
-
-
- .. py:attribute:: compartment
-
- Id (*value field*) Reac-diff compartment in which this diffusion system is embedded.
-
-
- .. py:attribute:: numVoxels
-
- unsigned int (*value field*) Number of voxels in the core reac-diff system, on the current diffusion solver.
-
-
- .. py:attribute:: numAllVoxels
-
- unsigned int (*value field*) Number of voxels in the core reac-diff system, on the current diffusion solver.
-
-
- .. py:attribute:: numPools
-
- unsigned int (*value field*) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.
-
-
- .. py:attribute:: nVec
-
- unsigned int,vector<double> (*lookup field*) vector of # of molecules along diffusion length, looked up by pool index
-
-
-.. py:class:: Enz
-
-
-.. py:class:: EnzBase
-
- Abstract base class for enzymes.
-
- .. py:attribute:: sub
-
- void (*shared message field*) Connects to substrate molecule
-
-
- .. py:attribute:: prd
-
- void (*shared message field*) Connects to product molecule
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setKm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getKm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumKm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumKm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setKcat
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getKcat
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumSubstrates
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: enzDest
-
- (*destination message field*) Handles # of molecules of Enzyme
-
-
- .. py:method:: subDest
-
- (*destination message field*) Handles # of molecules of substrate
-
-
- .. py:method:: prdDest
-
- (*destination message field*) Handles # of molecules of product. Dummy.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: remesh
-
- (*destination message field*) Tells the MMEnz to recompute its numKm after remeshing
-
-
- .. py:attribute:: subOut
-
- double,double (*source message field*) Sends out increment of molecules on product each timestep
-
-
- .. py:attribute:: prdOut
-
- double,double (*source message field*) Sends out increment of molecules on product each timestep
-
-
- .. py:attribute:: Km
-
- double (*value field*) Michaelis-Menten constant in SI conc units (milliMolar)
-
-
- .. py:attribute:: numKm
-
- double (*value field*) Michaelis-Menten constant in number units, volume dependent
-
-
- .. py:attribute:: kcat
-
- double (*value field*) Forward rate constant for enzyme, units 1/sec
-
-
- .. py:attribute:: numSubstrates
-
- unsigned int (*value field*) Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
-
-
-.. py:class:: Finfo
-
-
- .. py:method:: getFieldName
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDocs
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getType
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSrc
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDest
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: fieldName
-
- string (*value field*) Name of field handled by Finfo
-
-
- .. py:attribute:: docs
-
- string (*value field*) Documentation for Finfo
-
-
- .. py:attribute:: type
-
- string (*value field*) RTTI type info for this Finfo
-
-
- .. py:attribute:: src
-
- vector<string> (*value field*) Subsidiary SrcFinfos. Useful for SharedFinfos
-
-
- .. py:attribute:: dest
-
- vector<string> (*value field*) Subsidiary DestFinfos. Useful for SharedFinfos
-
-
-.. py:class:: Func
-
- Func: general purpose function calculator using real numbers. It can
- parse mathematical expression defining a function and evaluate it
- and/or its derivative for specified variable values.
- The variables can be input from other moose objects. In case of
- arbitrary variable names, the source message must have the variable
- name as the first argument. For most common cases, input messages to
- set x, y, z and xy, xyz are made available without such
- requirement. This class handles only real numbers
- (C-double). Predefined constants are: pi=3.141592...,
- e=2.718281...
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: getValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDerivative
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMode
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMode
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setExpr
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getExpr
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setVar
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVar
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getVars
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setX
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: varIn
-
- (*destination message field*) Handle value for specified variable coming from other objects
-
-
- .. py:method:: xIn
-
- (*destination message field*) Handle value for variable named x. This is a shorthand. If the
- expression does not have any variable named x, this the first variable
- in the sequence `vars`.
-
-
- .. py:method:: yIn
-
- (*destination message field*) Handle value for variable named y. This is a utility for two/three
- variable functions where the y value comes from a source separate
- from that of x. This is a shorthand. If the
- expression does not have any variable named y, this the second
- variable in the sequence `vars`.
-
-
- .. py:method:: zIn
-
- (*destination message field*) Handle value for variable named z. This is a utility for three
- variable functions where the z value comes from a source separate
- from that of x or y. This is a shorthand. If the expression does not
- have any variable named y, this the second variable in the sequence `vars`.
-
-
- .. py:method:: xyIn
-
- (*destination message field*) Handle value for variables x and y for two-variable function
-
-
- .. py:method:: xyzIn
-
- (*destination message field*) Handle value for variables x, y and z for three-variable function
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call, updates internal time stamp.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call.
-
-
- .. py:attribute:: valueOut
-
- double (*source message field*) Evaluated value of the function for the current variable values.
-
-
- .. py:attribute:: derivativeOut
-
- double (*source message field*) Value of derivative of the function for the current variable values
-
-
- .. py:attribute:: value
-
- double (*value field*) Result of the function evaluation with current variable values.
-
-
- .. py:attribute:: derivative
-
- double (*value field*) Derivative of the function at given variable values.
-
-
- .. py:attribute:: mode
-
- unsigned int (*value field*) Mode of operation:
- 1: only the function value will be calculated
- 2: only the derivative will be calculated
- 3: both function value and derivative at current variable values will be calculated.
-
-
- .. py:attribute:: expr
-
- string (*value field*) Mathematical expression defining the function. The underlying parser
- is muParser. Hence the available functions and operators are (from
- muParser docs):
-
- Functions
- Name args explanation
- sin 1 sine function
- cos 1 cosine function
- tan 1 tangens function
- asin 1 arcus sine function
- acos 1 arcus cosine function
- atan 1 arcus tangens function
- sinh 1 hyperbolic sine function
- cosh 1 hyperbolic cosine
- tanh 1 hyperbolic tangens function
- asinh 1 hyperbolic arcus sine function
- acosh 1 hyperbolic arcus tangens function
- atanh 1 hyperbolic arcur tangens function
- log2 1 logarithm to the base 2
- log10 1 logarithm to the base 10
- log 1 logarithm to the base 10
- ln 1 logarithm to base e (2.71828...)
- exp 1 e raised to the power of x
- sqrt 1 square root of a value
- sign 1 sign function -1 if x<0; 1 if x>0
- rint 1 round to nearest integer
- abs 1 absolute value
- min var. min of all arguments
- max var. max of all arguments
- sum var. sum of all arguments
- avg var. mean value of all arguments
-
- Operators
- Op meaning prioroty
- = assignement -1
- && logical and 1
- || logical or 2
- <= less or equal 4
- >= greater or equal 4
- != not equal 4
- == equal 4
- > greater than 4
- < less than 4
- + addition 5
- - subtraction 5
- * multiplication 6
- / division 6
- ^ raise x to the power of y 7
-
- ?: if then else operator C++ style syntax
-
-
-
- .. py:attribute:: vars
-
- vector<string> (*value field*) Variable names in the expression
-
-
- .. py:attribute:: x
-
- double (*value field*) Value for variable named x. This is a shorthand. If the
- expression does not have any variable named x, this the first variable
- in the sequence `vars`.
-
-
- .. py:attribute:: y
-
- double (*value field*) Value for variable named y. This is a utility for two/three
- variable functions where the y value comes from a source separate
- from that of x. This is a shorthand. If the
- expression does not have any variable named y, this the second
- variable in the sequence `vars`.
-
-
- .. py:attribute:: z
-
- double (*value field*) Value for variable named z. This is a utility for three
- variable functions where the z value comes from a source separate
- from that of x or z. This is a shorthand. If the expression does not
- have any variable named z, this the third variable in the sequence `vars`.
-
-
- .. py:attribute:: var
-
- string,double (*lookup field*) Lookup table for variable values.
-
-
-.. py:class:: FuncBase
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: getResult
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: input
-
- (*destination message field*) Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: output
-
- double (*source message field*) Sends out sum on each timestep
-
-
- .. py:attribute:: result
-
- double (*value field*) Outcome of function computation
-
-
-.. py:class:: FuncPool
-
-
- .. py:method:: input
-
- (*destination message field*) Handles input to control value of n\_
-
-
-.. py:class:: Function
-
- Function: general purpose function calculator using real numbers. It can parse mathematical expression defining a function and evaluate it and/or its derivative for specified variable values. The variables can be input from other moose objects. Such variables must be named `x{i}` in the expression and the source field is connected to Function.x[i]'s setVar destination field. In case the input variable is not available as a source field, but is a value field, then the value can be requested by connecting the `requestOut` message to the `get{Field}` destination on the target object. Such variables must be specified in the expression as y{i} and connecting the messages should happen in the same order as the y indices. This class handles only real numbers (C-double). Predefined constants are: pi=3.141592..., e=2.718281...
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: getValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getRate
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDerivative
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMode
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMode
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setExpr
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getExpr
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumX
-
- (*destination message field*) Assigns number of field entries in field array.
-
-
- .. py:method:: getNumX
-
- (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setC
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getC
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setIndependent
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getIndependent
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call, updates internal time stamp.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call.
-
-
- .. py:attribute:: requestOut
-
- PSt6vectorIdSaIdEE (*source message field*) Sends request for input variable from a field on target object
-
-
- .. py:attribute:: valueOut
-
- double (*source message field*) Evaluated value of the function for the current variable values.
-
-
- .. py:attribute:: rateOut
-
- double (*source message field*) Value of time-derivative of the function for the current variable values
-
-
- .. py:attribute:: derivativeOut
-
- double (*source message field*) Value of derivative of the function for the current variable values
-
-
- .. py:attribute:: value
-
- double (*value field*) Result of the function evaluation with current variable values.
-
-
- .. py:attribute:: rate
-
- double (*value field*) Derivative of the function at given variable values. This is computed as the difference of the current and previous value of the function divided by the time step.
-
-
- .. py:attribute:: derivative
-
- double (*value field*) Derivative of the function at given variable values. This is calulated using 5-point stencil <http://en.wikipedia.org/wiki/Five-point_stencil>__ at current value of independent variable. Note that unlike hand-calculated derivatives, numerical derivatives are not exact.
-
-
- .. py:attribute:: mode
-
- unsigned int (*value field*) Mode of operation::
-
- 1: only the function value will be sent out.
- 2: only the derivative with respect to the independent variable will be sent out.
- 3: only rate (time derivative) will be sent out.
- anything else: all three, value, derivative and rate will be sent out.
-
-
-
- .. py:attribute:: expr
-
- string (*value field*) Mathematical expression defining the function. The underlying parser
- is muParser. Hence the available functions and operators are (from
- muParser docs):
-
- Functions
- Name args explanation
- sin 1 sine function
- cos 1 cosine function
- tan 1 tangens function
- asin 1 arcus sine function
- acos 1 arcus cosine function
- atan 1 arcus tangens function
- sinh 1 hyperbolic sine function
- cosh 1 hyperbolic cosine
- tanh 1 hyperbolic tangens function
- asinh 1 hyperbolic arcus sine function
- acosh 1 hyperbolic arcus tangens function
- atanh 1 hyperbolic arcur tangens function
- log2 1 logarithm to the base 2
- log10 1 logarithm to the base 10
- log 1 logarithm to the base 10
- ln 1 logarithm to base e (2.71828...)
- exp 1 e raised to the power of x
- sqrt 1 square root of a value
- sign 1 sign function -1 if x<0; 1 if x>0
- rint 1 round to nearest integer
- abs 1 absolute value
- min var. min of all arguments
- max var. max of all arguments
- sum var. sum of all arguments
- avg var. mean value of all arguments
-
- Operators
- Op meaning prioroty
- = assignement -1
- && logical and 1
- || logical or 2
- <= less or equal 4
- >= greater or equal 4
- != not equal 4
- == equal 4
- > greater than 4
- < less than 4
- + addition 5
- - subtraction 5
- * multiplication 6
- / division 6
- ^ raise x to the power of y 7
-
- ?: if then else operator C++ style syntax
-
-
-
- .. py:attribute:: independent
-
- string (*value field*) Index of independent variable. Differentiation is done based on this. Defaults to the first assigned variable.
-
-
- .. py:attribute:: c
-
- string,double (*lookup field*) Constants used in the function. These must be assigned before specifying the function expression.
-
-
-.. py:class:: GapJunction
-
- Implementation of gap junction between two compartments. The shared
- fields, 'channel1' and 'channel2' can be connected to the 'channel'
- message of the compartments at either end of the gap junction. The
- compartments will send their Vm to the gap junction and receive the
- conductance 'Gk' of the gap junction and the Vm of the other
- compartment.
-
- .. py:attribute:: channel1
-
- void (*shared message field*) This is a shared message to couple the conductance and Vm from
- terminal 2 to the compartment at terminal 1. The first entry is source
- sending out Gk and Vm2, the second entry is destination for Vm1.
-
-
- .. py:attribute:: channel2
-
- void (*shared message field*) This is a shared message to couple the conductance and Vm from
- terminal 1 to the compartment at terminal 2. The first entry is source
- sending out Gk and Vm1, the second entry is destination for Vm2.
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process messages from the scheduler objects. The Process should be called *second* in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: Vm1
-
- (*destination message field*) Handles Vm message from compartment
-
-
- .. py:method:: Vm2
-
- (*destination message field*) Handles Vm message from another compartment
-
-
- .. py:method:: setGk
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getGk
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles 'process' call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles 'reinit' call
-
-
- .. py:attribute:: channel1Out
-
- double,double (*source message field*) Sends Gk and Vm from one compartment to the other
-
-
- .. py:attribute:: channel2Out
-
- double,double (*source message field*) Sends Gk and Vm from one compartment to the other
-
-
- .. py:attribute:: Gk
-
- double (*value field*) Conductance of the gap junction
-
-
-.. py:class:: Group
-
-
- .. py:attribute:: group
-
- void (*source message field*) Handle for grouping Elements
-
-
-.. py:class:: Gsolve
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setStoich
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStoich
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumLocalVoxels
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNVec
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNVec
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumAllVoxels
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumAllVoxels
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumPools
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumPools
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: voxelVol
-
- (*destination message field*) Handles updates to all voxels. Comes from parent ChemCompt object.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: setUseRandInit
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getUseRandInit
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: stoich
-
- Id (*value field*) Stoichiometry object for handling this reaction system.
-
-
- .. py:attribute:: numLocalVoxels
-
- unsigned int (*value field*) Number of voxels in the core reac-diff system, on the current solver.
-
-
- .. py:attribute:: numAllVoxels
-
- unsigned int (*value field*) Number of voxels in the entire reac-diff system, including proxy voxels to represent abutting compartments.
-
-
- .. py:attribute:: numPools
-
- unsigned int (*value field*) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.
-
-
- .. py:attribute:: useRandInit
-
- bool (*value field*) Flag: True when using probabilistic (random) rounding. When initializing the mol# from floating-point Sinit values, we have two options. One is to look at each Sinit, and round to the nearest integer. The other is to look at each Sinit, and probabilistically round up or down depending on the value. For example, if we had a Sinit value of 1.49, this would always be rounded to 1.0 if the flag is false, and would be rounded to 1.0 and 2.0 in the ratio 51:49 if the flag is true.
-
-
- .. py:attribute:: nVec
-
- unsigned int,vector<double> (*lookup field*) vector of pool counts
-
-
-.. py:class:: HDF5DataWriter
-
- HDF5 file writer for saving data tables. It saves the tables connected to it via `requestOut` field into an HDF5 file. The path of the table is maintained in the HDF5 file, with a HDF5 group for each element above the table.
- Thus, if you have a table `/data/VmTable` in MOOSE, then it will be written as an HDF5 table called `VmTable` inside an HDF5 Group called `data`.
- However Table inside Table is considered a pathological case and is not handled.
- At every process call it writes the contents of the tables to the file and clears the table vectors. You can explicitly force writing of the data via the `flush` function.
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message to receive process and reinit
-
-
- .. py:method:: setFlushLimit
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getFlushLimit
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handle process calls. Write data to file and clear all Table objects associated with this. Hence you want to keep it on a slow clock 1000 times or more slower than that for the tables.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Reinitialize the object. If the current file handle is valid, it tries to close that and open the file specified in current filename field.
-
-
- .. py:attribute:: requestOut
-
- PSt6vectorIdSaIdEE (*source message field*) Sends request for a field to target object
-
-
- .. py:attribute:: flushLimit
-
- unsigned int (*value field*) Buffer size limit for flushing the data from memory to file. Default is 4M doubles.
-
-
-.. py:class:: HDF5WriterBase
-
- HDF5 file writer base class. This is not to be used directly. Instead, it should be subclassed to provide specific data writing functions. This class provides most basic properties like filename, file opening mode, file open status.
-
- .. py:method:: setFilename
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getFilename
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getIsOpen
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMode
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMode
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setChunkSize
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getChunkSize
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCompressor
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCompressor
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCompression
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCompression
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setStringAttr
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStringAttr
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDoubleAttr
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDoubleAttr
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setLongAttr
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLongAttr
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setStringVecAttr
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStringVecAttr
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDoubleVecAttr
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDoubleVecAttr
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setLongVecAttr
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLongVecAttr
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: flush
-
- (*destination message field*) Write all buffer contents to file and clear the buffers.
-
-
- .. py:method:: close
-
- (*destination message field*) Close the underlying file. This is a safety measure so that file is not in an invalid state even if a crash happens at exit.
-
-
- .. py:attribute:: filename
-
- string (*value field*) Name of the file associated with this HDF5 writer object.
-
-
- .. py:attribute:: isOpen
-
- bool (*value field*) True if this object has an open file handle.
-
-
- .. py:attribute:: mode
-
- unsigned int (*value field*) Depending on mode, if file already exists, if mode=1, data will be appended to existing file, if mode=2, file will be truncated, if mode=4, no writing will happen.
-
-
- .. py:attribute:: chunkSize
-
- unsigned int (*value field*) Chunksize for writing array data. Defaults to 100.
-
-
- .. py:attribute:: compressor
-
- string (*value field*) Compression type for array data. zlib and szip are supported. Defaults to zlib.
-
-
- .. py:attribute:: compression
-
- unsigned int (*value field*) Compression level for array data. Defaults to 6.
-
-
- .. py:attribute:: stringAttr
-
- string,string (*lookup field*) String attributes. The key is attribute name, value is attribute value (string).
-
-
- .. py:attribute:: doubleAttr
-
- string,double (*lookup field*) Double precision floating point attributes. The key is attribute name, value is attribute value (double).
-
-
- .. py:attribute:: longAttr
-
- string,long (*lookup field*) Long integer attributes. The key is attribute name, value is attribute value (long).
-
-
- .. py:attribute:: stringVecAttr
-
- string,vector<string> (*lookup field*) String vector attributes. The key is attribute name, value is attribute value (string).
-
-
- .. py:attribute:: doubleVecAttr
-
- string,vector<double> (*lookup field*) Double vector attributes. The key is attribute name, value is attribute value (vector of double).
-
-
- .. py:attribute:: longVecAttr
-
- string,vector<long> (*lookup field*) Long integer vector attributes. The key is attribute name, value is attribute value (vector of long).
-
-
-.. py:class:: HHChannel
-
- HHChannel: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.
-
-.. py:class:: HHChannel2D
-
- HHChannel2D: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.
-
- .. py:method:: setXindex
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXindex
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYindex
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYindex
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZindex
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZindex
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXpower
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXpower
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYpower
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYpower
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZpower
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZpower
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInstant
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInstant
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setX
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: concen
-
- (*destination message field*) Incoming message from Concen object to specific conc to useas the first concen variable
-
-
- .. py:method:: concen2
-
- (*destination message field*) Incoming message from Concen object to specific conc to useas the second concen variable
-
-
- .. py:method:: setNumGateX
-
- (*destination message field*) Assigns number of field entries in field array.
-
-
- .. py:method:: getNumGateX
-
- (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumGateY
-
- (*destination message field*) Assigns number of field entries in field array.
-
-
- .. py:method:: getNumGateY
-
- (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumGateZ
-
- (*destination message field*) Assigns number of field entries in field array.
-
-
- .. py:method:: getNumGateZ
-
- (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: Xindex
-
- string (*value field*) String for setting X index.
-
-
- .. py:attribute:: Yindex
-
- string (*value field*) String for setting Y index.
-
-
- .. py:attribute:: Zindex
-
- string (*value field*) String for setting Z index.
-
-
- .. py:attribute:: Xpower
-
- double (*value field*) Power for X gate
-
-
- .. py:attribute:: Ypower
-
- double (*value field*) Power for Y gate
-
-
- .. py:attribute:: Zpower
-
- double (*value field*) Power for Z gate
-
-
- .. py:attribute:: instant
-
- int (*value field*) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state
-
-
- .. py:attribute:: X
-
- double (*value field*) State variable for X gate
-
-
- .. py:attribute:: Y
-
- double (*value field*) State variable for Y gate
-
-
- .. py:attribute:: Z
-
- double (*value field*) State variable for Y gate
-
-
-.. py:class:: HHChannelBase
-
- HHChannelBase: Base class for Hodgkin-Huxley type voltage-gated Ion channels. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.
-
- .. py:method:: setXpower
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXpower
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYpower
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYpower
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZpower
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZpower
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInstant
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInstant
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setX
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getX
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setY
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getY
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZ
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZ
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setUseConcentration
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getUseConcentration
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: concen
-
- (*destination message field*) Incoming message from Concen object to specific conc to usein the Z gate calculations
-
-
- .. py:method:: createGate
-
- (*destination message field*) Function to create specified gate.Argument: Gate type [X Y Z]
-
-
- .. py:method:: setNumGateX
-
- (*destination message field*) Assigns number of field entries in field array.
-
-
- .. py:method:: getNumGateX
-
- (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumGateY
-
- (*destination message field*) Assigns number of field entries in field array.
-
-
- .. py:method:: getNumGateY
-
- (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumGateZ
-
- (*destination message field*) Assigns number of field entries in field array.
-
-
- .. py:method:: getNumGateZ
-
- (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: Xpower
-
- double (*value field*) Power for X gate
-
-
- .. py:attribute:: Ypower
-
- double (*value field*) Power for Y gate
-
-
- .. py:attribute:: Zpower
-
- double (*value field*) Power for Z gate
-
-
- .. py:attribute:: instant
-
- int (*value field*) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state
-
-
- .. py:attribute:: X
-
- double (*value field*) State variable for X gate
-
-
- .. py:attribute:: Y
-
- double (*value field*) State variable for Y gate
-
-
- .. py:attribute:: Z
-
- double (*value field*) State variable for Y gate
-
-
- .. py:attribute:: useConcentration
-
- int (*value field*) Flag: when true, use concentration message rather than Vm tocontrol Z gate
-
-
-.. py:class:: HHGate
-
- HHGate: Gate for Hodkgin-Huxley type channels, equivalent to the m and h terms on the Na squid channel and the n term on K. This takes the voltage and state variable from the channel, computes the new value of the state variable and a scaling, depending on gate power, for the conductance.
-
- .. py:method:: getA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setAlpha
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getAlpha
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setBeta
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getBeta
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTau
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTau
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMInfinity
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMInfinity
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDivs
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDivs
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTableA
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTableA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTableB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTableB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setUseInterpolation
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getUseInterpolation
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setAlphaParms
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getAlphaParms
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setupAlpha
-
- (*destination message field*) Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
-
-
- .. py:method:: setupTau
-
- (*destination message field*) Identical to setupAlpha, except that the forms specified bythe 13 parameters are for the tau and m-infinity curves ratherthan the alpha and beta terms. So the parameters are:setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmaxAs before, the equation describing each curve is:y(x) = (A + B * x) / (C + exp((x + D) / F))
-
-
- .. py:method:: tweakAlpha
-
- (*destination message field*) Dummy function for backward compatibility. It used to convertthe tables from alpha, beta values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.
-
-
- .. py:method:: tweakTau
-
- (*destination message field*) Dummy function for backward compatibility. It used to convertthe tables from tau, minf values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.
-
-
- .. py:method:: setupGate
-
- (*destination message field*) Sets up one gate at a time using the alpha/beta form.Has 9 parameters, as follows:setupGate A B C D F xdivs xmin xmax is\_betaThis sets up the gate using the equation::
- y(x) = (A + B * x) / (C + exp((x + D) / F))
-
- *Deprecated.*
-
-
- .. py:attribute:: alpha
-
- vector<double> (*value field*) Parameters for voltage-dependent rates, alpha:Set up alpha term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
-
-
- .. py:attribute:: beta
-
- vector<double> (*value field*) Parameters for voltage-dependent rates, beta:Set up beta term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
-
-
- .. py:attribute:: tau
-
- vector<double> (*value field*) Parameters for voltage-dependent rates, tau:Set up tau curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))
-
-
- .. py:attribute:: mInfinity
-
- vector<double> (*value field*) Parameters for voltage-dependent rates, mInfinity:Set up mInfinity curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
-
-
- .. py:attribute:: min
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: max
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: divs
-
- unsigned int (*value field*) Divisions for lookup. Zero means to use linear interpolation
-
-
- .. py:attribute:: tableA
-
- vector<double> (*value field*) Table of A entries
-
-
- .. py:attribute:: tableB
-
- vector<double> (*value field*) Table of alpha + beta entries
-
-
- .. py:attribute:: useInterpolation
-
- bool (*value field*) Flag: use linear interpolation if true, else direct lookup
-
-
- .. py:attribute:: alphaParms
-
- vector<double> (*value field*) Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
-
-
- .. py:attribute:: A
-
- double,double (*lookup field*) lookupA: Look up the A gate value from a double. Usually doesso by direct scaling and offset to an integer lookup, usinga fine enough table granularity that there is little error.Alternatively uses linear interpolation.The range of the double is predefined based on knowledge ofvoltage or conc ranges, and the granularity is specified bythe xmin, xmax, and dV fields.
-
-
- .. py:attribute:: B
-
- double,double (*lookup field*) lookupB: Look up the B gate value from a double.Note that this looks up the raw tables, which are transformedfrom the reference parameters.
-
-
-.. py:class:: HHGate2D
-
- HHGate2D: Gate for Hodkgin-Huxley type channels, equivalent to the m and h terms on the Na squid channel and the n term on K. This takes the voltage and state variable from the channel, computes the new value of the state variable and a scaling, depending on gate power, for the conductance. These two terms are sent right back in a message to the channel.
-
- .. py:method:: getA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTableA
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTableA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTableB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTableB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXminA
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXminA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXmaxA
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmaxA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXdivsA
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXdivsA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYminA
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYminA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYmaxA
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYmaxA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYdivsA
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYdivsA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXminB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXminB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXmaxB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmaxB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXdivsB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXdivsB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYminB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYminB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYmaxB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYmaxB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYdivsB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYdivsB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: tableA
-
- vector< vector<double> > (*value field*) Table of A entries
-
-
- .. py:attribute:: tableB
-
- vector< vector<double> > (*value field*) Table of B entries
-
-
- .. py:attribute:: xminA
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: xmaxA
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: xdivsA
-
- unsigned int (*value field*) Divisions for lookup. Zero means to use linear interpolation
-
-
- .. py:attribute:: yminA
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: ymaxA
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: ydivsA
-
- unsigned int (*value field*) Divisions for lookup. Zero means to use linear interpolation
-
-
- .. py:attribute:: xminB
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: xmaxB
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: xdivsB
-
- unsigned int (*value field*) Divisions for lookup. Zero means to use linear interpolation
-
-
- .. py:attribute:: yminB
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: ymaxB
-
- double (*value field*) Minimum range for lookup
-
-
- .. py:attribute:: ydivsB
-
- unsigned int (*value field*) Divisions for lookup. Zero means to use linear interpolation
-
-
- .. py:attribute:: A
-
- vector<double>,double (*lookup field*) lookupA: Look up the A gate value from two doubles, passedin as a vector. Uses linear interpolation in the 2D tableThe range of the lookup doubles is predefined based on knowledge of voltage or conc ranges, and the granularity is specified by the xmin, xmax, and dx field, and their y-axis counterparts.
-
-
- .. py:attribute:: B
-
- vector<double>,double (*lookup field*) lookupB: Look up B gate value from two doubles in a vector.
-
-
-.. py:class:: HSolve
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Handles 'reinit' and 'process' calls from a clock.
-
-
- .. py:method:: setSeed
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSeed
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTarget
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTarget
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDt
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDt
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCaAdvance
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCaAdvance
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setVDiv
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVDiv
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setVMin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVMin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setVMax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVMax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCaDiv
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCaDiv
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCaMin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCaMin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCaMax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCaMax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles 'process' call: Solver advances by one time-step.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles 'reinit' call: Solver reads in model.
-
-
- .. py:attribute:: seed
-
- Id (*value field*) Use this field to specify path to a 'seed' compartment, that is, any compartment within a neuron. The HSolve object uses this seed as a handle to discover the rest of the neuronal model, which means all the remaining compartments, channels, synapses, etc.
-
-
- .. py:attribute:: target
-
- string (*value field*) Specifies the path to a compartmental model to be taken over. This can be the path to any container object that has the model under it (found by performing a deep search). Alternatively, this can also be the path to any compartment within the neuron. This compartment will be used as a handle to discover the rest of the model, which means all the remaining compartments, channels, synapses, etc.
-
-
- .. py:attribute:: dt
-
- double (*value field*) The time-step for this solver.
-
-
- .. py:attribute:: caAdvance
-
- int (*value field*) This flag determines how current flowing into a calcium pool is computed. A value of 0 means that the membrane potential at the beginning of the time-step is used for the calculation. This is how GENESIS does its computations. A value of 1 means the membrane potential at the middle of the time-step is used. This is the correct way of integration, and is the default way.
-
-
- .. py:attribute:: vDiv
-
- int (*value field*) Specifies number of divisions for lookup tables of voltage-sensitive channels.
-
-
- .. py:attribute:: vMin
-
- double (*value field*) Specifies the lower bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
-
-
- .. py:attribute:: vMax
-
- double (*value field*) Specifies the upper bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
-
-
- .. py:attribute:: caDiv
-
- int (*value field*) Specifies number of divisions for lookup tables of calcium-sensitive channels.
-
-
- .. py:attribute:: caMin
-
- double (*value field*) Specifies the lower bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
-
-
- .. py:attribute:: caMax
-
- double (*value field*) Specifies the upper bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
-
-
-.. py:class:: IntFire
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setVm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTau
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTau
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setThresh
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThresh
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRefractoryPeriod
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRefractoryPeriod
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: activation
-
- (*destination message field*) Handles value of synaptic activation arriving on this IntFire
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: spikeOut
-
- double (*source message field*) Sends out spike events. The argument is the timestamp of the spike.
-
-
- .. py:attribute:: Vm
-
- double (*value field*) Membrane potential
-
-
- .. py:attribute:: tau
-
- double (*value field*) charging time-course
-
-
- .. py:attribute:: thresh
-
- double (*value field*) firing threshold
-
-
- .. py:attribute:: refractoryPeriod
-
- double (*value field*) Minimum time between successive spikes
-
-
-.. py:class:: IntFireBase
-
- Base class for Integrate-and-fire compartment.
-
- .. py:method:: setThresh
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThresh
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRefractoryPeriod
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRefractoryPeriod
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getHasFired
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: activation
-
- (*destination message field*) Handles value of synaptic activation arriving on this object
-
-
- .. py:attribute:: spikeOut
-
- double (*source message field*) Sends out spike events. The argument is the timestamp of the spike.
-
-
- .. py:attribute:: thresh
-
- double (*value field*) firing threshold
-
-
- .. py:attribute:: refractoryPeriod
-
- double (*value field*) Minimum time between successive spikes
-
-
- .. py:attribute:: hasFired
-
- bool (*value field*) The object has fired within the last timestep
-
-
-.. py:class:: Interpol
-
- Interpol: Interpolation class. Handles lookup from a 1-dimensional array of real-numbered values.Returns 'y' value based on given 'x' value. Can either use interpolation or roundoff to the nearest index.
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setXmin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXmax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getY
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: input
-
- (*destination message field*) Interpolates using the input as x value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call, updates internal time stamp.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call.
-
-
- .. py:attribute:: lookupOut
-
- double (*source message field*) respond to a request for a value lookup
-
-
- .. py:attribute:: xmin
-
- double (*value field*) Minimum value of x. x below this will result in y[0] being returned.
-
-
- .. py:attribute:: xmax
-
- double (*value field*) Maximum value of x. x above this will result in y[last] being returned.
-
-
- .. py:attribute:: y
-
- double (*value field*) Looked up value.
-
-
-.. py:class:: Interpol2D
-
- Interpol2D: Interpolation class. Handles lookup from a 2-dimensional grid of real-numbered values. Returns 'z' value based on given 'x' and 'y' values. Can either use interpolation or roundoff to the nearest index.
-
- .. py:attribute:: lookupReturn2D
-
- void (*shared message field*) This is a shared message for doing lookups on the table. Receives 2 doubles: x, y. Sends back a double with the looked-up z value.
-
-
- .. py:method:: lookup
-
- (*destination message field*) Looks up table value based on indices v1 and v2, and sendsvalue back using the 'lookupOut' message
-
-
- .. py:method:: setXmin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXmax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXdivs
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXdivs
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDx
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDx
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYmin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYmin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYmax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYmax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYdivs
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYdivs
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDy
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDy
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTable
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTable
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getZ
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTableVector2D
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTableVector2D
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: lookupOut
-
- double (*source message field*) respond to a request for a value lookup
-
-
- .. py:attribute:: xmin
-
- double (*value field*) Minimum value for x axis of lookup table
-
-
- .. py:attribute:: xmax
-
- double (*value field*) Maximum value for x axis of lookup table
-
-
- .. py:attribute:: xdivs
-
- unsigned int (*value field*) # of divisions on x axis of lookup table
-
-
- .. py:attribute:: dx
-
- double (*value field*) Increment on x axis of lookup table
-
-
- .. py:attribute:: ymin
-
- double (*value field*) Minimum value for y axis of lookup table
-
-
- .. py:attribute:: ymax
-
- double (*value field*) Maximum value for y axis of lookup table
-
-
- .. py:attribute:: ydivs
-
- unsigned int (*value field*) # of divisions on y axis of lookup table
-
-
- .. py:attribute:: dy
-
- double (*value field*) Increment on y axis of lookup table
-
-
- .. py:attribute:: tableVector2D
-
- vector< vector<double> > (*value field*) Get the entire table.
-
-
- .. py:attribute:: table
-
- vector<unsigned int>,double (*lookup field*) Lookup an entry on the table
-
-
- .. py:attribute:: z
-
- vector<double>,double (*lookup field*) Interpolated value for specified x and y. This is provided for debugging. Normally other objects will retrieve interpolated values via lookup message.
-
-
-.. py:class:: IzhikevichNrn
-
- Izhikevich model of spiking neuron (Izhikevich,EM. 2003. Simple model of spiking neurons. Neural Networks, IEEE Transactions on 14(6). pp 1569-1572).
- This class obeys the equations (in physiological units):
- dVm/dt = 0.04 * Vm^2 + 5 * Vm + 140 - u + inject
- du/dt = a * (b * Vm - u)
- if Vm >= Vmax then Vm = c and u = u + d
- Vmax = 30 mV in the paper.
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message to receive Process message from scheduler
-
-
- .. py:attribute:: channel
-
- void (*shared message field*) This is a shared message from a IzhikevichNrn to channels.The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: setVmax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVmax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setC
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getC
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setD
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getD
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setA
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getA
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setB
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getB
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getU
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setVm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getIm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInject
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInject
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRmByTau
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRmByTau
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setAccommodating
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getAccommodating
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setU0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getU0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInitVm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInitVm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInitU
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInitU
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setAlpha
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getAlpha
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setBeta
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getBeta
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setGamma
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getGamma
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: injectMsg
-
- (*destination message field*) Injection current into the neuron.
-
-
- .. py:method:: cDest
-
- (*destination message field*) Destination message to modify parameter c at runtime.
-
-
- .. py:method:: dDest
-
- (*destination message field*) Destination message to modify parameter d at runtime.
-
-
- .. py:method:: bDest
-
- (*destination message field*) Destination message to modify parameter b at runtime
-
-
- .. py:method:: aDest
-
- (*destination message field*) Destination message modify parameter a at runtime.
-
-
- .. py:method:: handleChannel
-
- (*destination message field*) Handles conductance and reversal potential arguments from Channel
-
-
- .. py:attribute:: VmOut
-
- double (*source message field*) Sends out Vm
-
-
- .. py:attribute:: spikeOut
-
- double (*source message field*) Sends out spike events
-
-
- .. py:attribute:: VmOut
-
- double (*source message field*) Sends out Vm
-
-
- .. py:attribute:: Vmax
-
- double (*value field*) Maximum membrane potential. Membrane potential is reset to c whenever it reaches Vmax. NOTE: Izhikevich model specifies the PEAK voltage, rather than THRSHOLD voltage. The threshold depends on the previous history.
-
-
- .. py:attribute:: c
-
- double (*value field*) Reset potential. Membrane potential is reset to c whenever it reaches Vmax.
-
-
- .. py:attribute:: d
-
- double (*value field*) Parameter d in Izhikevich model. Unit is V/s.
-
-
- .. py:attribute:: a
-
- double (*value field*) Parameter a in Izhikevich model. Unit is s^{-1}
-
-
- .. py:attribute:: b
-
- double (*value field*) Parameter b in Izhikevich model. Unit is s^{-1}
-
-
- .. py:attribute:: u
-
- double (*value field*) Parameter u in Izhikevich equation. Unit is V/s
-
-
- .. py:attribute:: Vm
-
- double (*value field*) Membrane potential, equivalent to v in Izhikevich equation.
-
-
- .. py:attribute:: Im
-
- double (*value field*) Total current going through the membrane. Unit is A.
-
-
- .. py:attribute:: inject
-
- double (*value field*) External current injection into the neuron
-
-
- .. py:attribute:: RmByTau
-
- double (*value field*) Hidden coefficient of input current term (I) in Izhikevich model. Defaults to 1e9 Ohm/s.
-
-
- .. py:attribute:: accommodating
-
- bool (*value field*) True if this neuron is an accommodating one. The equation for recovery variable u is special in this case.
-
-
- .. py:attribute:: u0
-
- double (*value field*) This is used for accommodating neurons where recovery variables u is computed as: u += tau*a*(b*(Vm-u0))
-
-
- .. py:attribute:: initVm
-
- double (*value field*) Initial membrane potential. Unit is V.
-
-
- .. py:attribute:: initU
-
- double (*value field*) Initial value of u.
-
-
- .. py:attribute:: alpha
-
- double (*value field*) Coefficient of v^2 in Izhikevich equation. Defaults to 0.04 in physiological unit. In SI it should be 40000.0. Unit is V^-1 s^{-1}
-
-
- .. py:attribute:: beta
-
- double (*value field*) Coefficient of v in Izhikevich model. Defaults to 5 in physiological unit, 5000.0 for SI units. Unit is s^{-1}
-
-
- .. py:attribute:: gamma
-
- double (*value field*) Constant term in Izhikevich model. Defaults to 140 in both physiological and SI units. unit is V/s.
-
-
-.. py:class:: Ksolve
-
-
- .. py:attribute:: xCompt
-
- void (*shared message field*) Shared message for pool exchange for cross-compartment reactions. Exchanges latest values of all pools that participate in such reactions.
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit. These are used for all regular Ksolve calculations including interfacing with the diffusion calculations by a Dsolve.
-
-
- .. py:attribute:: init
-
- void (*shared message field*) Shared message for initProc and initReinit. This is used when the system has cross-compartment reactions.
-
-
- .. py:method:: setMethod
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMethod
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setEpsAbs
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getEpsAbs
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setEpsRel
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getEpsRel
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCompartment
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCompartment
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumLocalVoxels
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNVec
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNVec
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumAllVoxels
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumAllVoxels
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumPools
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumPools
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getEstimatedDt
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: voxelVol
-
- (*destination message field*) Handles updates to all voxels. Comes from parent ChemCompt object.
-
-
- .. py:method:: xComptIn
-
- (*destination message field*) Handles arriving pool 'n' values used in cross-compartment reactions.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call from Clock
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call from Clock
-
-
- .. py:method:: initProc
-
- (*destination message field*) Handles initProc call from Clock
-
-
- .. py:method:: initReinit
-
- (*destination message field*) Handles initReinit call from Clock
-
-
- .. py:attribute:: xComptOut
-
- Id,vector<double> (*source message field*) Sends 'n' of all molecules participating in cross-compartment reactions between any juxtaposed voxels between current compt and another compartment. This includes molecules local to this compartment, as well as proxy molecules belonging elsewhere. A(t+1) = (Alocal(t+1) + AremoteProxy(t+1)) - Alocal(t) A(t+1) = (Aremote(t+1) + Aproxy(t+1)) - Aproxy(t) Then we update A on the respective solvers with: Alocal(t+1) = Aproxy(t+1) = A(t+1) This is equivalent to sending dA over on each timestep.
-
-
- .. py:attribute:: method
-
- string (*value field*) Integration method, using GSL. So far only explict. Options are:rk5: The default Runge-Kutta-Fehlberg 5th order adaptive dt methodgsl: alias for the aboverk4: The Runge-Kutta 4th order fixed dt methodrk2: The Runge-Kutta 2,3 embedded fixed dt methodrkck: The Runge-Kutta Cash-Karp (4,5) methodrk8: The Runge-Kutta Prince-Dormand (8,9) method
-
-
- .. py:attribute:: epsAbs
-
- double (*value field*) Absolute permissible integration error range.
-
-
- .. py:attribute:: epsRel
-
- double (*value field*) Relative permissible integration error range.
-
-
- .. py:attribute:: compartment
-
- Id (*value field*) Compartment in which the Ksolve reaction system lives.
-
-
- .. py:attribute:: numLocalVoxels
-
- unsigned int (*value field*) Number of voxels in the core reac-diff system, on the current solver.
-
-
- .. py:attribute:: numAllVoxels
-
- unsigned int (*value field*) Number of voxels in the entire reac-diff system, including proxy voxels to represent abutting compartments.
-
-
- .. py:attribute:: numPools
-
- unsigned int (*value field*) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.
-
-
- .. py:attribute:: estimatedDt
-
- double (*value field*) Estimated timestep for reac system based on Euler error
-
-
- .. py:attribute:: nVec
-
- unsigned int,vector<double> (*lookup field*) vector of pool counts. Index specifies which voxel.
-
-
-.. py:class:: LIF
-
- Leaky Integrate-and-Fire neuron
-
-.. py:class:: Leakage
-
- Leakage: Passive leakage channel.
-
-.. py:class:: MMenz
-
-
-.. py:class:: MarkovChannel
-
- MarkovChannel : Multistate ion channel class.It deals with ion channels which can be found in one of multiple states, some of which are conducting. This implementation assumes the occurence of first order kinetics to calculate the probabilities of the channel being found in all states. Further, the rates of transition between these states can be constant, voltage-dependent or ligand dependent (only one ligand species). The current flow obtained from the channel is calculated in a deterministic method by solving the system of differential equations obtained from the assumptions above.
-
- .. py:method:: setLigandConc
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLigandConc
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setVm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumStates
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumStates
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumOpenStates
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumOpenStates
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getState
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInitialState
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInitialState
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setLabels
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLabels
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setGbar
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getGbar
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: handleLigandConc
-
- (*destination message field*) Deals with incoming messages containing information of ligand concentration
-
-
- .. py:method:: handleState
-
- (*destination message field*) Deals with incoming message from MarkovSolver object containing state information of the channel.
-
-
-
- .. py:attribute:: ligandConc
-
- double (*value field*) Ligand concentration.
-
-
- .. py:attribute:: Vm
-
- double (*value field*) Membrane voltage.
-
-
- .. py:attribute:: numStates
-
- unsigned int (*value field*) The number of states that the channel can occupy.
-
-
- .. py:attribute:: numOpenStates
-
- unsigned int (*value field*) The number of states which are open/conducting.
-
-
- .. py:attribute:: state
-
- vector<double> (*value field*) This is a row vector that contains the probabilities of finding the channel in each state.
-
-
- .. py:attribute:: initialState
-
- vector<double> (*value field*) This is a row vector that contains the probabilities of finding the channel in each state at t = 0. The state of the channel is reset to this value during a call to reinit()
-
-
- .. py:attribute:: labels
-
- vector<string> (*value field*) Labels for each state.
-
-
- .. py:attribute:: gbar
-
- vector<double> (*value field*) A row vector containing the conductance associated with each of the open/conducting states.
-
-
-.. py:class:: MarkovGslSolver
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: getIsInitialized
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMethod
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMethod
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRelativeAccuracy
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRelativeAccuracy
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setAbsoluteAccuracy
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getAbsoluteAccuracy
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInternalDt
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInternalDt
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: init
-
- (*destination message field*) Initialize solver parameters.
-
-
- .. py:method:: handleQ
-
- (*destination message field*) Handles information regarding the instantaneous rate matrix from the MarkovRateTable class.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: stateOut
-
- vector<double> (*source message field*) Sends updated state to the MarkovChannel class.
-
-
- .. py:attribute:: isInitialized
-
- bool (*value field*) True if the message has come in to set solver parameters.
-
-
- .. py:attribute:: method
-
- string (*value field*) Numerical method to use.
-
-
- .. py:attribute:: relativeAccuracy
-
- double (*value field*) Accuracy criterion
-
-
- .. py:attribute:: absoluteAccuracy
-
- double (*value field*) Another accuracy criterion
-
-
- .. py:attribute:: internalDt
-
- double (*value field*) internal timestep to use.
-
-
-.. py:class:: MarkovRateTable
-
-
- .. py:attribute:: channel
-
- void (*shared message field*) This message couples the rate table to the compartment. The rate table needs updates on voltage in order to compute the rate table.
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: handleVm
-
- (*destination message field*) Handles incoming message containing voltage information.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: init
-
- (*destination message field*) Initialization of the class. Allocates memory for all the tables.
-
-
- .. py:method:: handleLigandConc
-
- (*destination message field*) Handles incoming message containing ligand concentration.
-
-
- .. py:method:: set1d
-
- (*destination message field*) Setting up of 1D lookup table for the (i,j)'th rate.
-
-
- .. py:method:: set2d
-
- (*destination message field*) Setting up of 2D lookup table for the (i,j)'th rate.
-
-
- .. py:method:: setconst
-
- (*destination message field*) Setting a constant value for the (i,j)'th rate. Internally, this is stored as a 1-D rate with a lookup table containing 1 entry.
-
-
- .. py:method:: setVm
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVm
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setLigandConc
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLigandConc
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getQ
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSize
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: instratesOut
-
- vector< vector<double> > (*source message field*) Sends out instantaneous rate information of varying transition ratesat each time step.
-
-
- .. py:attribute:: Vm
-
- double (*value field*) Membrane voltage.
-
-
- .. py:attribute:: ligandConc
-
- double (*value field*) Ligand concentration.
-
-
- .. py:attribute:: Q
-
- vector< vector<double> > (*value field*) Instantaneous rate matrix.
-
-
- .. py:attribute:: size
-
- unsigned int (*value field*) Dimension of the families of lookup tables. Is always equal to the number of states in the model.
-
-
-.. py:class:: MarkovSolver
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
-.. py:class:: MarkovSolverBase
-
-
- .. py:attribute:: channel
-
- void (*shared message field*) This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: handleVm
-
- (*destination message field*) Handles incoming message containing voltage information.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: ligandConc
-
- (*destination message field*) Handles incoming message containing ligand concentration.
-
-
- .. py:method:: init
-
- (*destination message field*) Setups the table of matrix exponentials associated with the solver object.
-
-
- .. py:method:: getQ
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getState
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInitialState
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInitialState
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXmin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXmax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXdivs
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXdivs
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getInvdx
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYmin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYmin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYmax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYmax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setYdivs
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getYdivs
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getInvdy
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: stateOut
-
- vector<double> (*source message field*) Sends updated state to the MarkovChannel class.
-
-
- .. py:attribute:: Q
-
- vector< vector<double> > (*value field*) Instantaneous rate matrix.
-
-
- .. py:attribute:: state
-
- vector<double> (*value field*) Current state of the channel.
-
-
- .. py:attribute:: initialState
-
- vector<double> (*value field*) Initial state of the channel.
-
-
- .. py:attribute:: xmin
-
- double (*value field*) Minimum value for x axis of lookup table
-
-
- .. py:attribute:: xmax
-
- double (*value field*) Maximum value for x axis of lookup table
-
-
- .. py:attribute:: xdivs
-
- unsigned int (*value field*) # of divisions on x axis of lookup table
-
-
- .. py:attribute:: invdx
-
- double (*value field*) Reciprocal of increment on x axis of lookup table
-
-
- .. py:attribute:: ymin
-
- double (*value field*) Minimum value for y axis of lookup table
-
-
- .. py:attribute:: ymax
-
- double (*value field*) Maximum value for y axis of lookup table
-
-
- .. py:attribute:: ydivs
-
- unsigned int (*value field*) # of divisions on y axis of lookup table
-
-
- .. py:attribute:: invdy
-
- double (*value field*) Reciprocal of increment on y axis of lookup table
-
-
-.. py:class:: MathFunc
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setMathML
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMathML
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setFunction
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getFunction
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getResult
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: arg1
-
- (*destination message field*) Handle arg1
-
-
- .. py:method:: arg2
-
- (*destination message field*) Handle arg2
-
-
- .. py:method:: arg3
-
- (*destination message field*) Handle arg3
-
-
- .. py:method:: arg4
-
- (*destination message field*) Handle arg4
-
-
- .. py:method:: process
-
- (*destination message field*) Handle process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handle reinit call
-
-
- .. py:attribute:: output
-
- double (*source message field*) Sends out result of computation
-
-
- .. py:attribute:: mathML
-
- string (*value field*) MathML version of expression to compute
-
-
- .. py:attribute:: function
-
- string (*value field*) function is for functions of form f(x, y) = x + y
-
-
- .. py:attribute:: result
-
- double (*value field*) result value
-
-
-.. py:class:: MeshEntry
-
- One voxel in a chemical reaction compartment
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:attribute:: mesh
-
- void (*shared message field*) Shared message for updating mesh volumes and subdivisions,typically controls pool volumes
-
-
- .. py:method:: getVolume
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDimensions
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getMeshType
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getCoordinates
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNeighbors
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDiffusionArea
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDiffusionScaling
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: getVolume
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: remeshOut
-
- double,unsigned int,unsigned int,vector<unsigned int>,vector<double> (*source message field*) Tells the target pool or other entity that the compartment subdivision(meshing) has changed, and that it has to redo its volume and memory allocation accordingly.Arguments are: oldvol, numTotalEntries, startEntry, localIndices, volsThe vols specifies volumes of each local mesh entry. It also specifieshow many meshEntries are present on the local node.The localIndices vector is used for general load balancing only.It has a list of the all meshEntries on current node.If it is empty, we assume block load balancing. In this secondcase the contents of the current node go from startEntry to startEntry + vols.size().
-
-
- .. py:attribute:: remeshReacsOut
-
- void (*source message field*) Tells connected enz or reac that the compartment subdivision(meshing) has changed, and that it has to redo its volume-dependent rate terms like numKf\_ accordingly.
-
-
- .. py:attribute:: volume
-
- double (*value field*) Volume of this MeshEntry
-
-
- .. py:attribute:: dimensions
-
- unsigned int (*value field*) number of dimensions of this MeshEntry
-
-
- .. py:attribute:: meshType
-
- unsigned int (*value field*) The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder 3. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral
-
-
- .. py:attribute:: Coordinates
-
- vector<double> (*value field*) Coordinates that define current MeshEntry. Depend on MeshType.
-
-
- .. py:attribute:: neighbors
-
- vector<unsigned int> (*value field*) Indices of other MeshEntries that this one connects to
-
-
- .. py:attribute:: DiffusionArea
-
- vector<double> (*value field*) Diffusion area for geometry of interface
-
-
- .. py:attribute:: DiffusionScaling
-
- vector<double> (*value field*) Diffusion scaling for geometry of interface
-
-
-.. py:class:: MgBlock
-
- MgBlock: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.
-
- .. py:method:: origChannel
-
- (*destination message field*)
-
-
- .. py:method:: setKMg_A
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getKMg_A
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setKMg_B
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getKMg_B
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCMg
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCMg
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setZk
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getZk
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: KMg_A
-
- double (*value field*) 1/eta
-
-
- .. py:attribute:: KMg_B
-
- double (*value field*) 1/gamma
-
-
- .. py:attribute:: CMg
-
- double (*value field*) [Mg] in mM
-
-
- .. py:attribute:: Zk
-
- double (*value field*) Charge on ion
-
-
-.. py:class:: Msg
-
-
- .. py:method:: getE1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getE2
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSrcFieldsOnE1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDestFieldsOnE2
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSrcFieldsOnE2
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDestFieldsOnE1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getAdjacent
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: e1
-
- Id (*value field*) Id of source Element.
-
-
- .. py:attribute:: e2
-
- Id (*value field*) Id of source Element.
-
-
- .. py:attribute:: srcFieldsOnE1
-
- vector<string> (*value field*) Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector
-
-
- .. py:attribute:: destFieldsOnE2
-
- vector<string> (*value field*) Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector
-
-
- .. py:attribute:: srcFieldsOnE2
-
- vector<string> (*value field*) Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector
-
-
- .. py:attribute:: destFieldsOnE1
-
- vector<string> (*value field*) Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
-
-
- .. py:attribute:: adjacent
-
- ObjId,ObjId (*lookup field*) The element adjacent to the specified element
-
-
-.. py:class:: Mstring
-
-
- .. py:method:: setThis
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThis
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setValue
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: this
-
- string (*value field*) Access function for entire Mstring object.
-
-
- .. py:attribute:: value
-
- string (*value field*) Access function for value field of Mstring object,which happens also to be the entire contents of the object.
-
-
-.. py:class:: Nernst
-
-
- .. py:method:: getE
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTemperature
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTemperature
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setValence
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getValence
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCout
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCout
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setScale
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getScale
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: ci
-
- (*destination message field*) Set internal conc of ion, and immediately send out the updated E
-
-
- .. py:method:: co
-
- (*destination message field*) Set external conc of ion, and immediately send out the updated E
-
-
- .. py:attribute:: Eout
-
- double (*source message field*) Computed reversal potential
-
-
- .. py:attribute:: E
-
- double (*value field*) Computed reversal potential
-
-
- .. py:attribute:: Temperature
-
- double (*value field*) Temperature of cell
-
-
- .. py:attribute:: valence
-
- int (*value field*) Valence of ion in Nernst calculation
-
-
- .. py:attribute:: Cin
-
- double (*value field*) Internal conc of ion
-
-
- .. py:attribute:: Cout
-
- double (*value field*) External conc of ion
-
-
- .. py:attribute:: scale
-
- double (*value field*) Voltage scale factor
-
-
-.. py:class:: NeuroMesh
-
-
- .. py:method:: setCell
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCell
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSubTree
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSubTree
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSeparateSpines
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSeparateSpines
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumSegments
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumDiffCompts
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getParentVoxel
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getElecComptList
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getElecComptMap
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getStartVoxelInCompt
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getEndVoxelInCompt
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDiffLength
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDiffLength
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setGeometryPolicy
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getGeometryPolicy
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: cellPortion
-
- (*destination message field*) Tells NeuroMesh to mesh up a subpart of a cell. For nowassumed contiguous.The first argument is the cell Id. The second is the wildcardpath of compartments to use for the subpart.
-
-
- .. py:attribute:: spineListOut
-
- Id,vector<Id>,vector<Id>,vector<unsigned int> (*source message field*) Request SpineMesh to construct self based on list of electrical compartments that this NeuroMesh has determined are spine shaft and spine head respectively. Also passes in the info about where each spine is connected to the NeuroMesh. Arguments: Cell Id, shaft compartment Ids, head compartment Ids,index of matching parent voxels for each spine
-
-
- .. py:attribute:: psdListOut
-
- Id,vector<double>,vector<unsigned int> (*source message field*) Tells PsdMesh to build a mesh. Arguments: Cell Id, Coordinates of each psd, index of matching parent voxels for each spineThe coordinates each have 8 entries:xyz of centre of psd, xyz of vector perpendicular to psd, psd diameter, diffusion distance from parent compartment to PSD
-
-
- .. py:attribute:: cell
-
- Id (*value field*) Id for base element of cell model. Uses this to traverse theentire tree of the cell to build the mesh.
-
-
- .. py:attribute:: subTree
-
- vector<Id> (*value field*) Set of compartments to model. If they happen to be contiguousthen also set up diffusion between the compartments. Can alsohandle cases where the same cell is divided into multiplenon-diffusively-coupled compartments
-
-
- .. py:attribute:: separateSpines
-
- bool (*value field*) Flag: when separateSpines is true, the traversal separates any compartment with the strings 'spine', 'head', 'shaft' or 'neck' in its name,Allows to set up separate mesh for spines, based on the same cell model. Requires for the spineListOut message tobe sent to the target SpineMesh object.
-
-
- .. py:attribute:: numSegments
-
- unsigned int (*value field*) Number of cylindrical/spherical segments in model
-
-
- .. py:attribute:: numDiffCompts
-
- unsigned int (*value field*) Number of diffusive compartments in model
-
-
- .. py:attribute:: parentVoxel
-
- vector<unsigned int> (*value field*) Vector of indices of parents of each voxel.
-
-
- .. py:attribute:: elecComptList
-
- vector<Id> (*value field*) Vector of Ids of all electrical compartments in this NeuroMesh. Ordering is as per the tree structure built in the NeuroMesh, and may differ from Id order. Ordering matches that used for startVoxelInCompt and endVoxelInCompt
-
-
- .. py:attribute:: elecComptMap
-
- vector<Id> (*value field*) Vector of Ids of electrical compartments that map to each voxel. This is necessary because the order of the IDs may differ from the ordering of the voxels. Additionally, there are typically many more voxels than there are electrical compartments. So many voxels point to the same elecCompt.
-
-
- .. py:attribute:: startVoxelInCompt
-
- vector<unsigned int> (*value field*) Index of first voxel that maps to each electrical compartment. Each elecCompt has one or more voxels. The voxels in a compartment are numbered sequentially.
-
-
- .. py:attribute:: endVoxelInCompt
-
- vector<unsigned int> (*value field*) Index of end voxel that maps to each electrical compartment. In keeping with C and Python convention, this is one more than the last voxel. Each elecCompt has one or more voxels. The voxels in a compartment are numbered sequentially.
-
-
- .. py:attribute:: diffLength
-
- double (*value field*) Diffusive length constant to use for subdivisions. The system willattempt to subdivide cell using diffusive compartments ofthe specified diffusion lengths as a maximum.In order to get integral numbersof compartments in each segment, it may subdivide more finely.Uses default of 0.5 microns, that is, half typical lambda.For default, consider a tau of about 1 second for mostreactions, and a diffusion const of about 1e-12 um^2/sec.This gives lambda of 1 micron
-
-
- .. py:attribute:: geometryPolicy
-
- string (*value field*) Policy for how to interpret electrical model geometry (which is a branching 1-dimensional tree) in terms of 3-D constructslike spheres, cylinders, and cones.There are three options, default, trousers, and cylinder:default mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites and dendrites emerging from soma, proximal diameter is from compt dia. Don't worry about overlap. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.trousers mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites, use a trouser function. Avoid overlap. - For soma, use some variant of trousers. Here we must avoid overlap - For spines, use a way to smoothly merge into parent dend. Radius of curvature should be similar to that of the spine neck. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.cylinder mode: - Use cylinders. Diameter is just compartment dia. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle. - Ignore spatial overlap.
-
-
-.. py:class:: Neuron
-
- Neuron - A compartment container
-
-.. py:class:: Neutral
-
- Neutral: Base class for all MOOSE classes. Providesaccess functions for housekeeping fields and operations, messagetraversal, and so on.
-
- .. py:method:: parentMsg
-
- (*destination message field*) Message from Parent Element(s)
-
-
- .. py:method:: setThis
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThis
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setName
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getName
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getMe
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getParent
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getChildren
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getPath
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getClassName
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumData
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumData
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumField
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumField
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTick
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTick
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDt
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getValueFields
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSourceFields
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDestFields
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getMsgOut
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getMsgIn
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNeighbors
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getMsgDests
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getMsgDestFunctions
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: childOut
-
- int (*source message field*) Message to child Elements
-
-
- .. py:attribute:: this
-
- Neutral (*value field*) Access function for entire object
-
-
- .. py:attribute:: name
-
- string (*value field*) Name of object
-
-
- .. py:attribute:: me
-
- ObjId (*value field*) ObjId for current object
-
-
- .. py:attribute:: parent
-
- ObjId (*value field*) Parent ObjId for current object
-
-
- .. py:attribute:: children
-
- vector<Id> (*value field*) vector of ObjIds listing all children of current object
-
-
- .. py:attribute:: path
-
- string (*value field*) text path for object
-
-
- .. py:attribute:: className
-
- string (*value field*) Class Name of object
-
-
- .. py:attribute:: numData
-
- unsigned int (*value field*) # of Data entries on Element.Note that on a FieldElement this does NOT refer to field entries,but to the number of DataEntries on the parent of the FieldElement.
-
-
- .. py:attribute:: numField
-
- unsigned int (*value field*) For a FieldElement: number of entries of self.For a regular Element: One.
-
-
- .. py:attribute:: tick
-
- int (*value field*) Clock tick for this Element for periodic execution in the main simulation event loop. A default is normally assigned, based on object class, but one can override to any value between 0 and 19. Assigning to -1 means that the object is disabled and will not be called during simulation execution The actual timestep (dt) belonging to a clock tick is defined by the Clock object.
-
-
- .. py:attribute:: dt
-
- double (*value field*) Timestep used for this Element. Zero if not scheduled.
-
-
- .. py:attribute:: valueFields
-
- vector<string> (*value field*) List of all value fields on Element.These fields are accessed through the assignment operations in the Python interface.These fields may also be accessed as functions through the set<FieldName> and get<FieldName> commands.
-
-
- .. py:attribute:: sourceFields
-
- vector<string> (*value field*) List of all source fields on Element, that is fields that can act as message sources.
-
-
- .. py:attribute:: destFields
-
- vector<string> (*value field*) List of all destination fields on Element, that is, fieldsthat are accessed as Element functions.
-
-
- .. py:attribute:: msgOut
-
- vector<ObjId> (*value field*) Messages going out from this Element
-
-
- .. py:attribute:: msgIn
-
- vector<ObjId> (*value field*) Messages coming in to this Element
-
-
- .. py:attribute:: neighbors
-
- string,vector<Id> (*lookup field*) Ids of Elements connected this Element on specified field.
-
-
- .. py:attribute:: msgDests
-
- string,vector<ObjId> (*lookup field*) ObjIds receiving messages from the specified SrcFinfo
-
-
- .. py:attribute:: msgDestFunctions
-
- string,vector<string> (*lookup field*) Matching function names for each ObjId receiving a msg from the specified SrcFinfo
-
-
-.. py:class:: OneToAllMsg
-
-
- .. py:method:: setI1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getI1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: i1
-
- unsigned int (*value field*) DataId of source Element.
-
-
-.. py:class:: OneToOneDataIndexMsg
-
-
-.. py:class:: OneToOneMsg
-
-
-.. py:class:: PIDController
-
- PID feedback controller.PID stands for Proportional-Integral-Derivative. It is used to feedback control dynamical systems. It tries to create a feedback output such that the sensed (measured) parameter is held at command value. Refer to wikipedia (http://wikipedia.org) for details on PID Controller.
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: setGain
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getGain
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSaturation
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSaturation
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCommand
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCommand
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSensed
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTauI
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTauI
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTauD
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTauD
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getOutputValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getError
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getIntegral
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getDerivative
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getE_previous
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: commandIn
-
- (*destination message field*) Command (desired value) input. This is known as setpoint (SP) in control theory.
-
-
- .. py:method:: sensedIn
-
- (*destination message field*) Sensed parameter - this is the one to be tuned. This is known as process variable (PV) in control theory. This comes from the process we are trying to control.
-
-
- .. py:method:: gainDest
-
- (*destination message field*) Destination message to control the PIDController gain dynamically.
-
-
- .. py:method:: process
-
- (*destination message field*) Handle process calls.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Reinitialize the object.
-
-
- .. py:attribute:: output
-
- double (*source message field*) Sends the output of the PIDController. This is known as manipulated variable (MV) in control theory. This should be fed into the process which we are trying to control.
-
-
- .. py:attribute:: gain
-
- double (*value field*) This is the proportional gain (Kp). This tuning parameter scales the proportional term. Larger gain usually results in faster response, but too much will lead to instability and oscillation.
-
-
- .. py:attribute:: saturation
-
- double (*value field*) Bound on the permissible range of output. Defaults to maximum double value.
-
-
- .. py:attribute:: command
-
- double (*value field*) The command (desired) value of the sensed parameter. In control theory this is commonly known as setpoint(SP).
-
-
- .. py:attribute:: sensed
-
- double (*value field*) Sensed (measured) value. This is commonly known as process variable(PV) in control theory.
-
-
- .. py:attribute:: tauI
-
- double (*value field*) The integration time constant, typically = dt. This is actually proportional gain divided by integral gain (Kp/Ki)). Larger Ki (smaller tauI) usually leads to fast elimination of steady state errors at the cost of larger overshoot.
-
-
- .. py:attribute:: tauD
-
- double (*value field*) The differentiation time constant, typically = dt / 4. This is derivative gain (Kd) times proportional gain (Kp). Larger Kd (tauD) decreases overshoot at the cost of slowing down transient response and may lead to instability.
-
-
- .. py:attribute:: outputValue
-
- double (*value field*) Output of the PIDController. This is given by::
- gain * ( error + INTEGRAL[ error dt ] / tau_i + tau_d * d(error)/dt )
-
- Where gain = proportional gain (Kp), tau\_i = integral gain (Kp/Ki) and tau\_d = derivative gain (Kd/Kp). In control theory this is also known as the manipulated variable (MV)
-
-
- .. py:attribute:: error
-
- double (*value field*) The error term, which is the difference between command and sensed value.
-
-
- .. py:attribute:: integral
-
- double (*value field*) The integral term. It is calculated as INTEGRAL(error dt) = previous\_integral + dt * (error + e\_previous)/2.
-
-
- .. py:attribute:: derivative
-
- double (*value field*) The derivative term. This is (error - e\_previous)/dt.
-
-
- .. py:attribute:: e_previous
-
- double (*value field*) The error term for previous step.
-
-
-.. py:class:: Pool
-
-
- .. py:method:: increment
-
- (*destination message field*) Increments mol numbers by specified amount. Can be +ve or -ve
-
-
- .. py:method:: decrement
-
- (*destination message field*) Decrements mol numbers by specified amount. Can be +ve or -ve
-
-
-.. py:class:: PoolBase
-
- Abstract base class for pools.
-
- .. py:attribute:: reac
-
- void (*shared message field*) Connects to reaction
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:attribute:: species
-
- void (*shared message field*) Shared message for connecting to species objects
-
-
- .. py:method:: setN
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getN
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNInit
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNInit
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDiffConst
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDiffConst
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMotorConst
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMotorConst
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setConc
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getConc
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setConcInit
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getConcInit
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setVolume
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVolume
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSpeciesId
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSpeciesId
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: reacDest
-
- (*destination message field*) Handles reaction input
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: handleMolWt
-
- (*destination message field*) Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
-
-
- .. py:attribute:: nOut
-
- double (*source message field*) Sends out # of molecules in pool on each timestep
-
-
- .. py:attribute:: requestMolWt
-
- void (*source message field*) Requests Species object for mol wt
-
-
- .. py:attribute:: n
-
- double (*value field*) Number of molecules in pool
-
-
- .. py:attribute:: nInit
-
- double (*value field*) Initial value of number of molecules in pool
-
-
- .. py:attribute:: diffConst
-
- double (*value field*) Diffusion constant of molecule
-
-
- .. py:attribute:: motorConst
-
- double (*value field*) Motor transport rate molecule. + is away from soma, - is towards soma. Only relevant for ZombiePool subclasses.
-
-
- .. py:attribute:: conc
-
- double (*value field*) Concentration of molecules in this pool
-
-
- .. py:attribute:: concInit
-
- double (*value field*) Initial value of molecular concentration in pool
-
-
- .. py:attribute:: volume
-
- double (*value field*) Volume of compartment. Units are SI. Utility field, the actual volume info is stored on a volume mesh entry in the parent compartment.This mapping is implicit: the parent compartment must be somewhere up the element tree, and must have matching mesh entries. If the compartment isn'tavailable the volume is just taken as 1
-
-
- .. py:attribute:: speciesId
-
- unsigned int (*value field*) Species identifier for this mol pool. Eventually link to ontology.
-
-
-.. py:class:: PostMaster
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: getNumNodes
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getMyNode
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setBufferSize
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getBufferSize
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: numNodes
-
- unsigned int (*value field*) Returns number of nodes that simulation runs on.
-
-
- .. py:attribute:: myNode
-
- unsigned int (*value field*) Returns index of current node.
-
-
- .. py:attribute:: bufferSize
-
- unsigned int (*value field*) Size of the send a receive buffers for each node.
-
-
-.. py:class:: PsdMesh
-
-
- .. py:method:: setThickness
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThickness
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: psdList
-
- (*destination message field*) Specifies the geometry of the spine,and the associated parent voxelArguments: cell container, disk params vector with 8 entriesper psd, parent voxel index
-
-
- .. py:attribute:: thickness
-
- double (*value field*) An assumed thickness for PSD. The volume is computed as thePSD area passed in to each PSD, times this value.defaults to 50 nanometres. For reference, membranes are 5 nm.
-
-
-.. py:class:: PulseGen
-
- PulseGen: general purpose pulse generator. This can generate any number of pulses with specified level and duration.
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: getOutputValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setBaseLevel
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getBaseLevel
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setFirstLevel
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getFirstLevel
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setFirstWidth
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getFirstWidth
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setFirstDelay
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getFirstDelay
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSecondLevel
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSecondLevel
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSecondWidth
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSecondWidth
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSecondDelay
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSecondDelay
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCount
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCount
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTrigMode
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTrigMode
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setLevel
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLevel
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setWidth
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getWidth
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDelay
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDelay
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: input
-
- (*destination message field*) Handle incoming input that determines gating/triggering onset. Note that although this is a double field, the underlying field is integer. So fractional part of input will be truncated
-
-
- .. py:method:: levelIn
-
- (*destination message field*) Handle level value coming from other objects
-
-
- .. py:method:: widthIn
-
- (*destination message field*) Handle width value coming from other objects
-
-
- .. py:method:: delayIn
-
- (*destination message field*) Handle delay value coming from other objects
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call, updates internal time stamp.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call.
-
-
- .. py:attribute:: output
-
- double (*source message field*) Current output level.
-
-
- .. py:attribute:: outputValue
-
- double (*value field*) Output amplitude
-
-
- .. py:attribute:: baseLevel
-
- double (*value field*) Basal level of the stimulus
-
-
- .. py:attribute:: firstLevel
-
- double (*value field*) Amplitude of the first pulse in a sequence
-
-
- .. py:attribute:: firstWidth
-
- double (*value field*) Width of the first pulse in a sequence
-
-
- .. py:attribute:: firstDelay
-
- double (*value field*) Delay to start of the first pulse in a sequence
-
-
- .. py:attribute:: secondLevel
-
- double (*value field*) Amplitude of the second pulse in a sequence
-
-
- .. py:attribute:: secondWidth
-
- double (*value field*) Width of the second pulse in a sequence
-
-
- .. py:attribute:: secondDelay
-
- double (*value field*) Delay to start of of the second pulse in a sequence
-
-
- .. py:attribute:: count
-
- unsigned int (*value field*) Number of pulses in a sequence
-
-
- .. py:attribute:: trigMode
-
- unsigned int (*value field*) Trigger mode for pulses in the sequence.
- 0 : free-running mode where it keeps looping its output
- 1 : external trigger, where it is triggered by an external input (and stops after creating the first train of pulses)
- 2 : external gate mode, where it keeps generating the pulses in a loop as long as the input is high.
-
-
- .. py:attribute:: level
-
- unsigned int,double (*lookup field*) Level of the pulse at specified index
-
-
- .. py:attribute:: width
-
- unsigned int,double (*lookup field*) Width of the pulse at specified index
-
-
- .. py:attribute:: delay
-
- unsigned int,double (*lookup field*) Delay of the pulse at specified index
-
-
-.. py:class:: RC
-
- RC circuit: a series resistance R shunted by a capacitance C.
-
- .. py:attribute:: proc
-
- void (*shared message field*) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
-
-
- .. py:method:: setV0
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getV0
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setR
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getR
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setC
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getC
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getState
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setInject
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getInject
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: injectIn
-
- (*destination message field*) Receives input to the RC circuit. All incoming messages are summed up to give the total input current.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handle reinitialization
-
-
- .. py:attribute:: output
-
- double (*source message field*) Current output level.
-
-
- .. py:attribute:: V0
-
- double (*value field*) Initial value of 'state'
-
-
- .. py:attribute:: R
-
- double (*value field*) Series resistance of the RC circuit.
-
-
- .. py:attribute:: C
-
- double (*value field*) Parallel capacitance of the RC circuit.
-
-
- .. py:attribute:: state
-
- double (*value field*) Output value of the RC circuit. This is the voltage across the capacitor.
-
-
- .. py:attribute:: inject
-
- double (*value field*) Input value to the RC circuit.This is handled as an input current to the circuit.
-
-
-.. py:class:: RandSpike
-
- RandSpike object, generates random spikes at.specified mean rate. Based closely on GENESIS randspike.
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message to receive Process message from scheduler
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: setRate
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRate
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRefractT
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRefractT
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setAbs_refract
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getAbs_refract
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getHasFired
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: spikeOut
-
- double (*source message field*) Sends out a trigger for an event.
-
-
- .. py:attribute:: rate
-
- double (*value field*) Specifies rate for random spike train. Note that this isprobabilistic, so the instantaneous rate may differ. If the rate is assigned be message and it varies slowly then the average firing rate will approach the specified rate
-
-
- .. py:attribute:: refractT
-
- double (*value field*) Refractory Time.
-
-
- .. py:attribute:: abs_refract
-
- double (*value field*) Absolute refractory time. Synonym for refractT.
-
-
- .. py:attribute:: hasFired
-
- bool (*value field*) True if RandSpike has just fired
-
-
-.. py:class:: Reac
-
-
-.. py:class:: ReacBase
-
- Base class for reactions. Provides the MOOSE APIfunctions, but ruthlessly refers almost all of them to derivedclasses, which have to provide the man page output.
-
- .. py:attribute:: sub
-
- void (*shared message field*) Connects to substrate pool
-
-
- .. py:attribute:: prd
-
- void (*shared message field*) Connects to substrate pool
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setNumKf
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumKf
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumKb
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumKb
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setKf
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getKf
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setKb
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getKb
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumSubstrates
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumProducts
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: subDest
-
- (*destination message field*) Handles # of molecules of substrate
-
-
- .. py:method:: prdDest
-
- (*destination message field*) Handles # of molecules of product
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: subOut
-
- double,double (*source message field*) Sends out increment of molecules on product each timestep
-
-
- .. py:attribute:: prdOut
-
- double,double (*source message field*) Sends out increment of molecules on product each timestep
-
-
- .. py:attribute:: numKf
-
- double (*value field*) Forward rate constant, in # units
-
-
- .. py:attribute:: numKb
-
- double (*value field*) Reverse rate constant, in # units
-
-
- .. py:attribute:: Kf
-
- double (*value field*) Forward rate constant, in concentration units
-
-
- .. py:attribute:: Kb
-
- double (*value field*) Reverse rate constant, in concentration units
-
-
- .. py:attribute:: numSubstrates
-
- unsigned int (*value field*) Number of substrates of reaction
-
-
- .. py:attribute:: numProducts
-
- unsigned int (*value field*) Number of products of reaction
-
-
-.. py:class:: Shell
-
-
- .. py:method:: setclock
-
- (*destination message field*) Assigns clock ticks. Args: tick#, dt
-
-
- .. py:method:: create
-
- (*destination message field*) create( class, parent, newElm, name, numData, isGlobal )
-
-
- .. py:method:: delete
-
- (*destination message field*) Destroys Element, all its messages, and all its children. Args: Id
-
-
- .. py:method:: copy
-
- (*destination message field*) handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): The vector< Id > has Id orig, Id newParent, Id newElm. This function copies an Element and all its children to a new parent. May also expand out the original into nCopies copies. Normally all messages within the copy tree are also copied. If the flag copyExtMsgs is true, then all msgs going out are also copied.
-
-
- .. py:method:: move
-
- (*destination message field*) handleMove( Id orig, Id newParent ): moves an Element to a new parent
-
-
- .. py:method:: addMsg
-
- (*destination message field*) Makes a msg. Arguments are: msgtype, src object, src field, dest object, dest field
-
-
- .. py:method:: quit
-
- (*destination message field*) Stops simulation running and quits the simulator
-
-
- .. py:method:: useClock
-
- (*destination message field*) Deals with assignment of path to a given clock. Arguments: path, field, tick number.
-
-
-.. py:class:: SimpleSynHandler
-
- The SimpleSynHandler handles simple synapses without plasticity. It uses a priority queue to manage them.
-
-.. py:class:: SingleMsg
-
-
- .. py:method:: setI1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getI1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setI2
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getI2
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: i1
-
- unsigned int (*value field*) Index of source object.
-
-
- .. py:attribute:: i2
-
- unsigned int (*value field*) Index of dest object.
-
-
-.. py:class:: SparseMsg
-
-
- .. py:method:: getNumRows
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumColumns
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumEntries
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setProbability
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getProbability
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setSeed
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getSeed
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRandomConnectivity
-
- (*destination message field*) Assigns connectivity with specified probability and seed
-
-
- .. py:method:: setEntry
-
- (*destination message field*) Assigns single row,column value
-
-
- .. py:method:: unsetEntry
-
- (*destination message field*) Clears single row,column entry
-
-
- .. py:method:: clear
-
- (*destination message field*) Clears out the entire matrix
-
-
- .. py:method:: transpose
-
- (*destination message field*) Transposes the sparse matrix
-
-
- .. py:method:: pairFill
-
- (*destination message field*) Fills entire matrix using pairs of (x,y) indices to indicate presence of a connection. If the target is a FieldElement itautomagically assigns FieldIndices.
-
-
- .. py:method:: tripletFill
-
- (*destination message field*) Fills entire matrix using triplets of (x,y,fieldIndex) to fully specify every connection in the sparse matrix.
-
-
- .. py:attribute:: numRows
-
- unsigned int (*value field*) Number of rows in matrix.
-
-
- .. py:attribute:: numColumns
-
- unsigned int (*value field*) Number of columns in matrix.
-
-
- .. py:attribute:: numEntries
-
- unsigned int (*value field*) Number of Entries in matrix.
-
-
- .. py:attribute:: probability
-
- double (*value field*) connection probability for random connectivity.
-
-
- .. py:attribute:: seed
-
- long (*value field*) Random number seed for generating probabilistic connectivity.
-
-
-.. py:class:: Species
-
-
- .. py:attribute:: pool
-
- void (*shared message field*) Connects to pools of this Species type
-
-
- .. py:method:: setMolWt
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMolWt
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: handleMolWtRequest
-
- (*destination message field*) Handle requests for molWt.
-
-
- .. py:attribute:: molWtOut
-
- double (*source message field*) returns molWt.
-
-
- .. py:attribute:: molWt
-
- double (*value field*) Molecular weight of species
-
-
-.. py:class:: SpikeGen
-
- SpikeGen object, for detecting threshold crossings.The threshold detection can work in multiple modes.
- If the refractT < 0.0, then it fires an event only at the rising edge of the input voltage waveform
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message to receive Process message from scheduler
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:method:: Vm
-
- (*destination message field*) Handles Vm message coming in from compartment
-
-
- .. py:method:: setThreshold
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThreshold
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setRefractT
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getRefractT
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setAbs_refract
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getAbs_refract
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getHasFired
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setEdgeTriggered
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getEdgeTriggered
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: spikeOut
-
- double (*source message field*) Sends out a trigger for an event.
-
-
- .. py:attribute:: threshold
-
- double (*value field*) Spiking threshold, must cross it going up
-
-
- .. py:attribute:: refractT
-
- double (*value field*) Refractory Time.
-
-
- .. py:attribute:: abs_refract
-
- double (*value field*) Absolute refractory time. Synonym for refractT.
-
-
- .. py:attribute:: hasFired
-
- bool (*value field*) True if SpikeGen has just fired
-
-
- .. py:attribute:: edgeTriggered
-
- bool (*value field*) When edgeTriggered = 0, the SpikeGen will fire an event in each timestep while incoming Vm is > threshold and at least abs\_refracttime has passed since last event. This may be problematic if the incoming Vm remains above threshold for longer than abs\_refract. Setting edgeTriggered to 1 resolves this as the SpikeGen generatesan event only on the rising edge of the incoming Vm and will remain idle unless the incoming Vm goes below threshold.
-
-
-.. py:class:: SpikeStats
-
- Object to do some minimal stats on rate of a spike train. Derived from the Stats object and returns the same set of stats.Can take either predigested spike event input, or can handle a continuous sampling of membrane potential Vm and decide if a spike has occured based on a threshold.
-
- .. py:method:: setThreshold
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThreshold
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: addSpike
-
- (*destination message field*) Handles spike event time input, converts into a rate to do stats upon.
-
-
- .. py:method:: Vm
-
- (*destination message field*) Handles continuous voltage input, can be coming in much than update rate of the SpikeStats. Looks for transitions above threshold to register the arrival of a spike. Doesn't do another spike till Vm falls below threshold.
-
-
- .. py:attribute:: threshold
-
- double (*value field*) Spiking threshold. If Vm crosses this going up then the SpikeStats object considers that a spike has happened and adds it to the stats.
-
-
-.. py:class:: SpineMesh
-
-
- .. py:method:: getParentVoxel
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: spineList
-
- (*destination message field*) Specifies the list of electrical compartments for the spine,and the associated parent voxelArguments: cell container, shaft compartments, head compartments, parent voxel index
-
-
- .. py:attribute:: parentVoxel
-
- vector<unsigned int> (*value field*) Vector of indices of proximal voxels within this mesh.Spines are at present modeled with just one compartment,so each entry in this vector is always set to EMPTY == -1U
-
-
-.. py:class:: Stats
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: getMean
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSdev
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSum
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNum
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getWmean
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getWsdev
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getWsum
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getWnum
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setWindowLength
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getWindowLength
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: input
-
- (*destination message field*) Handles continuous value input as a time-series. Multiple inputs are allowed, they will be merged.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: requestOut
-
- PSt6vectorIdSaIdEE (*source message field*) Sends request for a field to target object
-
-
- .. py:attribute:: mean
-
- double (*value field*) Mean of all sampled values or of spike rate.
-
-
- .. py:attribute:: sdev
-
- double (*value field*) Standard Deviation of all sampled values, or of rate.
-
-
- .. py:attribute:: sum
-
- double (*value field*) Sum of all sampled values, or total number of spikes.
-
-
- .. py:attribute:: num
-
- unsigned int (*value field*) Number of all sampled values, or total number of spikes.
-
-
- .. py:attribute:: wmean
-
- double (*value field*) Mean of sampled values or of spike rate within window.
-
-
- .. py:attribute:: wsdev
-
- double (*value field*) Standard Deviation of sampled values, or rate, within window.
-
-
- .. py:attribute:: wsum
-
- double (*value field*) Sum of all sampled values, or total number of spikes, within window.
-
-
- .. py:attribute:: wnum
-
- unsigned int (*value field*) Number of all sampled values, or total number of spikes, within window.
-
-
- .. py:attribute:: windowLength
-
- unsigned int (*value field*) Number of bins for windowed stats. Ignores windowing if this value is zero.
-
-
-.. py:class:: SteadyState
-
- SteadyState: works out a steady-state value for a reaction system. This class uses the GSL multidimensional root finder algorithms to find the fixed points closest to the current molecular concentrations. When it finds the fixed points, it figures out eigenvalues of the solution, as a way to help classify the fixed points. Note that the method finds unstable as well as stable fixed points.
- The SteadyState class also provides a utility function *randomInit()* to randomly initialize the concentrations, within the constraints of stoichiometry. This is useful if you are trying to find the major fixed points of the system. Note that this is probabilistic. If a fixed point is in a very narrow range of state space the probability of finding it is small and you will have to run many iterations with different initial conditions to find it.
- The numerical calculations used by the SteadyState solver are prone to failing on individual calculations. All is not lost, because the system reports the solutionStatus. It is recommended that you test this field after every calculation, so you can simply ignore cases where it failed and try again with different starting conditions.
- Another rule of thumb is that the SteadyState object is more likely to succeed in finding solutions from a new starting point if you numerically integrate the chemical system for a short time (typically under 1 second) before asking it to find the fixed point.
-
- .. py:method:: setStoich
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStoich
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getBadStoichiometry
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getIsInitialized
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNIter
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getStatus
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMaxIter
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMaxIter
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setConvergenceCriterion
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getConvergenceCriterion
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumVarPools
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getRank
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getStateType
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNNegEigenvalues
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNPosEigenvalues
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSolutionStatus
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTotal
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTotal
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getEigenvalues
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setupMatrix
-
- (*destination message field*) This function initializes and rebuilds the matrices used in the calculation.
-
-
- .. py:method:: settle
-
- (*destination message field*) Finds the nearest steady state to the current initial conditions. This function rebuilds the entire calculation only if the object has not yet been initialized.
-
-
- .. py:method:: resettle
-
- (*destination message field*) Finds the nearest steady state to the current initial conditions. This function rebuilds the entire calculation
-
-
- .. py:method:: showMatrices
-
- (*destination message field*) Utility function to show the matrices derived for the calculations on the reaction system. Shows the Nr, gamma, and total matrices
-
-
- .. py:method:: randomInit
-
- (*destination message field*) Generate random initial conditions consistent with the massconservation rules. Typically invoked in order to scanstates
-
-
- .. py:attribute:: stoich
-
- Id (*value field*) Specify the Id of the stoichiometry system to use
-
-
- .. py:attribute:: badStoichiometry
-
- bool (*value field*) Bool: True if there is a problem with the stoichiometry
-
-
- .. py:attribute:: isInitialized
-
- bool (*value field*) True if the model has been initialized successfully
-
-
- .. py:attribute:: nIter
-
- unsigned int (*value field*) Number of iterations done by steady state solver
-
-
- .. py:attribute:: status
-
- string (*value field*) Status of solver
-
-
- .. py:attribute:: maxIter
-
- unsigned int (*value field*) Max permissible number of iterations to try before giving up
-
-
- .. py:attribute:: convergenceCriterion
-
- double (*value field*) Fractional accuracy required to accept convergence
-
-
- .. py:attribute:: numVarPools
-
- unsigned int (*value field*) Number of variable molecules in reaction system.
-
-
- .. py:attribute:: rank
-
- unsigned int (*value field*) Number of independent molecules in reaction system
-
-
- .. py:attribute:: stateType
-
- unsigned int (*value field*) 0: stable; 1: unstable; 2: saddle; 3: osc?; 4: one near-zero eigenvalue; 5: other
-
-
- .. py:attribute:: nNegEigenvalues
-
- unsigned int (*value field*) Number of negative eigenvalues: indicates type of solution
-
-
- .. py:attribute:: nPosEigenvalues
-
- unsigned int (*value field*) Number of positive eigenvalues: indicates type of solution
-
-
- .. py:attribute:: solutionStatus
-
- unsigned int (*value field*) 0: Good; 1: Failed to find steady states; 2: Failed to find eigenvalues
-
-
- .. py:attribute:: total
-
- unsigned int,double (*lookup field*) Totals table for conservation laws. The exact mapping ofthis to various sums of molecules is given by the conservation matrix, and is currently a bit opaque.The value of 'total' is set to initial conditions whenthe 'SteadyState::settle' function is called.Assigning values to the total is a special operation:it rescales the concentrations of all the affectedmolecules so that they are at the specified total.This happens the next time 'settle' is called.
-
-
- .. py:attribute:: eigenvalues
-
- unsigned int,double (*lookup field*) Eigenvalues computed for steady state
-
-
-.. py:class:: StimulusTable
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setStartTime
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStartTime
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setStopTime
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStopTime
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setLoopTime
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getLoopTime
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setStepSize
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStepSize
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setStepPosition
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getStepPosition
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDoLoop
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDoLoop
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call, updates internal time stamp.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call.
-
-
- .. py:attribute:: output
-
- double (*source message field*) Sends out tabulated data according to lookup parameters.
-
-
- .. py:attribute:: startTime
-
- double (*value field*) Start time used when table is emitting values. For lookupvalues below this, the table just sends out its zero entry.Corresponds to zeroth entry of table.
-
-
- .. py:attribute:: stopTime
-
- double (*value field*) Time to stop emitting values.If time exceeds this, then the table sends out its last entry.The stopTime corresponds to the last entry of table.
-
-
- .. py:attribute:: loopTime
-
- double (*value field*) If looping, this is the time between successive cycle starts.Defaults to the difference between stopTime and startTime, so that the output waveform cycles with precisely the same duration as the table contents.If larger than stopTime - startTime, then it pauses at the last table value till it is time to go around again.If smaller than stopTime - startTime, then it begins the next cycle even before the first one has reached the end of the table.
-
-
- .. py:attribute:: stepSize
-
- double (*value field*) Increment in lookup (x) value on every timestep. If it isless than or equal to zero, the StimulusTable uses the current timeas the lookup value.
-
-
- .. py:attribute:: stepPosition
-
- double (*value field*) Current value of lookup (x) value.If stepSize is less than or equal to zero, this is set tothe current time to use as the lookup value.
-
-
- .. py:attribute:: doLoop
-
- bool (*value field*) Flag: Should it loop around to startTime once it has reachedstopTime. Default (zero) is to do a single pass.
-
-
-.. py:class:: Stoich
-
-
- .. py:method:: setPath
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getPath
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setKsolve
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getKsolve
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDsolve
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDsolve
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setCompartment
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getCompartment
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumVarPools
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumAllPools
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumProxyPools
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getPoolIdMap
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getNumRates
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getMatrixEntry
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getColumnIndex
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getRowStart
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getProxyPools
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: unzombify
-
- (*destination message field*) Restore all zombies to their native state
-
-
- .. py:method:: buildXreacs
-
- (*destination message field*) Build cross-reaction terms between current stoich and argument. This function scans the voxels at which there are junctions between different compartments, and orchestrates set up of interfaces between the Ksolves that implement the X reacs at those junctions.
-
-
- .. py:method:: filterXreacs
-
- (*destination message field*) Filter cross-reaction terms on current stoichThis function clears out absent rate terms that would otherwise try to compute cross reactions where the junctions are not present.
-
-
- .. py:attribute:: path
-
- string (*value field*) Wildcard path for reaction system handled by Stoich
-
-
- .. py:attribute:: ksolve
-
- Id (*value field*) Id of Kinetic reaction solver class that works with this Stoich. Must be of class Ksolve, or Gsolve (at present) Must be assigned before the path is set.
-
-
- .. py:attribute:: dsolve
-
- Id (*value field*) Id of Diffusion solver class that works with this Stoich. Must be of class Dsolve If left unset then the system will be assumed to work in a non-diffusive, well-stirred cell. If it is going to be used it must be assigned before the path is set.
-
-
- .. py:attribute:: compartment
-
- Id (*value field*) Id of chemical compartment class that works with this Stoich. Must be derived from class ChemCompt. If left unset then the system will be assumed to work in a non-diffusive, well-stirred cell. If it is going to be used it must be assigned before the path is set.
-
-
- .. py:attribute:: numVarPools
-
- unsigned int (*value field*) Number of time-varying pools to be computed by the numerical engine
-
-
- .. py:attribute:: numAllPools
-
- unsigned int (*value field*) Total number of pools handled by the numerical engine. This includes variable ones, buffered ones, and functions
-
-
- .. py:attribute:: numProxyPools
-
- unsigned int (*value field*) Number of pools here by proxy as substrates of a cross-compartment reaction.
-
-
- .. py:attribute:: poolIdMap
-
- vector<unsigned int> (*value field*) Map to look up the index of the pool from its Id.poolIndex = poolIdMap[ Id::value() - poolOffset ] where the poolOffset is the smallest Id::value. poolOffset is passed back as the last entry of this vector. Any Ids that are not pools return EMPTY=~0.
-
-
- .. py:attribute:: numRates
-
- unsigned int (*value field*) Total number of rate terms in the reaction system.
-
-
- .. py:attribute:: matrixEntry
-
- vector<int> (*value field*) The non-zero matrix entries in the sparse matrix. Theircolumn indices are in a separate vector and the rowinformatino in a third
-
-
- .. py:attribute:: columnIndex
-
- vector<unsigned int> (*value field*) Column Index of each matrix entry
-
-
- .. py:attribute:: rowStart
-
- vector<unsigned int> (*value field*) Row start for each block of entries and column indices
-
-
- .. py:attribute:: proxyPools
-
- Id,vector<Id> (*lookup field*) Return vector of proxy pools for X-compt reactions between current stoich, and the argument, which is a StoichId. The returned pools belong to the compartment handling the Stoich specified in the argument. If no pools are found, return an empty vector.
-
-
-.. py:class:: SumFunc
-
- SumFunc object. Adds up all inputs
-
-.. py:class:: SymCompartment
-
- SymCompartment object, for branching neuron models. In symmetric
- compartments the axial resistance is equally divided on two sides of
- the node. The equivalent circuit of the passive compartment becomes:
- (NOTE: you must use a fixed-width font like Courier for correct rendition of the diagrams below)::
-
- Ra/2 B Ra/2
- A-/\/\/\_____/\/\/\-- C
- |
- ____|____
- | |
- | \
- | / Rm
- ---- Cm \
- ---- /
- | |
- | _____
- | --- Em
- |_________|
- |
- __|__
- /////
-
-
- In case of branching, the B-C part of the parent's axial resistance
- forms a Y with the A-B part of the children::
- B'
- |
- /
- \
- /
- \
- /
- |A'
- B |
- A-----/\/\/\-----/\/\/\------|C
- |
- |A"
- /
- \
- /
- \
- /
- |
- B"
- As per basic circuit analysis techniques, the C node is replaced using
- star-mesh transform. This requires all sibling compartments at a
- branch point to be connected via 'sibling' messages by the user (or
- by the cell reader in case of prototypes). For the same reason, the
- child compartment must be connected to the parent by
- distal-proximal message pair. The calculation of the
- coefficient for computing equivalent resistances in the mesh is done
- at reinit.
-
- .. py:attribute:: proximal
-
- void (*shared message field*) This is a shared message between symmetric compartments.
- It goes from the proximal end of the current compartment to
- distal end of the compartment closer to the soma.
-
-
-
- .. py:attribute:: distal
-
- void (*shared message field*) This is a shared message between symmetric compartments.
- It goes from the distal end of the current compartment to the
- proximal end of one further from the soma.
- The Ra values collected from children and
- sibling nodes are used for computing the equivalent resistance
- between each pair of nodes using star-mesh transformation.
- Mathematically this is the same as the proximal message, but
- the distinction is important for traversal and clarity.
-
-
-
- .. py:attribute:: sibling
-
- void (*shared message field*) This is a shared message between symmetric compartments.
- Conceptually, this goes from the proximal end of the current
- compartment to the proximal end of a sibling compartment
- on a branch in a dendrite. However,
- this works out to the same as a 'distal' message in terms of
- equivalent circuit. The Ra values collected from siblings
- and parent node are used for
- computing the equivalent resistance between each pair of
- nodes using star-mesh transformation.
-
-
-
- .. py:attribute:: sphere
-
- void (*shared message field*) This is a shared message between a spherical compartment
- (typically soma) and a number of evenly spaced cylindrical
- compartments, typically primary dendrites.
- The sphere contributes the usual Ra/2 to the resistance
- between itself and children. The child compartments
- do not connect across to each other
- through sibling messages. Instead they just connect to the soma
- through the 'proximalOnly' message
-
-
-
- .. py:attribute:: cylinder
-
- void (*shared message field*) This is a shared message between a cylindrical compartment
- (typically a dendrite) and a number of evenly spaced child
- compartments, typically dendritic spines, protruding from the
- curved surface of the cylinder. We assume that the resistance
- from the cylinder curved surface to its axis is negligible.
- The child compartments do not need to connect across to each
- other through sibling messages. Instead they just connect to the
- parent dendrite through the 'proximalOnly' message
-
-
-
- .. py:attribute:: proximalOnly
-
- void (*shared message field*) This is a shared message between a dendrite and a parent
- compartment whose offspring are spatially separated from each
- other. For example, evenly spaced dendrites emerging from a soma
- or spines emerging from a common parent dendrite. In these cases
- the sibling dendrites do not need to connect to each other
- through 'sibling' messages. Instead they just connect to the
- parent compartment (soma or dendrite) through this message
-
-
-
- .. py:method:: raxialSym
-
- (*destination message field*) Expects Ra and Vm from other compartment.
-
-
- .. py:method:: sumRaxial
-
- (*destination message field*) Expects Ra from other compartment.
-
-
- .. py:method:: raxialSym
-
- (*destination message field*) Expects Ra and Vm from other compartment.
-
-
- .. py:method:: sumRaxial
-
- (*destination message field*) Expects Ra from other compartment.
-
-
- .. py:method:: raxialSym
-
- (*destination message field*) Expects Ra and Vm from other compartment.
-
-
- .. py:method:: sumRaxial
-
- (*destination message field*) Expects Ra from other compartment.
-
-
- .. py:method:: raxialSphere
-
- (*destination message field*) Expects Ra and Vm from other compartment. This is a special case when other compartments are evenly distributed on a spherical compartment.
-
-
- .. py:method:: raxialCylinder
-
- (*destination message field*) Expects Ra and Vm from other compartment. This is a special case when other compartments are evenly distributed on the curved surface of the cylindrical compartment, so we assume that the cylinder does not add any further resistance.
-
-
- .. py:method:: raxialSphere
-
- (*destination message field*) Expects Ra and Vm from other compartment. This is a special case when other compartments are evenly distributed on a spherical compartment.
-
-
- .. py:attribute:: proximalOut
-
- double,double (*source message field*) Sends out Ra and Vm on each timestep, on the proximal end of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOut but provides a logical orientation of the dendrite. One can traverse proximalOut messages to get to the soma.
-
-
- .. py:attribute:: sumRaxialOut
-
- double (*source message field*) Sends out Ra
-
-
- .. py:attribute:: distalOut
-
- double,double (*source message field*) Sends out Ra and Vm on each timestep, on the distal end of a compartment. This end should be pointed away from the soma. Mathematically the same as proximalOut, but gives an orientation to the dendrite and helps traversal.
-
-
- .. py:attribute:: sumRaxialOut
-
- double (*source message field*) Sends out Ra
-
-
- .. py:attribute:: distalOut
-
- double,double (*source message field*) Sends out Ra and Vm on each timestep, on the distal end of a compartment. This end should be pointed away from the soma. Mathematically the same as proximalOut, but gives an orientation to the dendrite and helps traversal.
-
-
- .. py:attribute:: sumRaxialOut
-
- double (*source message field*) Sends out Ra
-
-
- .. py:attribute:: distalOut
-
- double,double (*source message field*) Sends out Ra and Vm on each timestep, on the distal end of a compartment. This end should be pointed away from the soma. Mathematically the same as proximalOut, but gives an orientation to the dendrite and helps traversal.
-
-
- .. py:attribute:: cylinderOut
-
- double,double (*source message field*) Sends out Ra and Vm to compartments (typically spines) on the curved surface of a cylinder. Ra is set to nearly zero, since we assume that the resistance from axis to surface is negligible.
-
-
- .. py:attribute:: proximalOut
-
- double,double (*source message field*) Sends out Ra and Vm on each timestep, on the proximal end of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOut but provides a logical orientation of the dendrite. One can traverse proximalOut messages to get to the soma.
-
-
-.. py:class:: SynChan
-
- SynChan: Synaptic channel incorporating weight and delay. Does not handle actual arrival of synaptic events, that is done by one of the derived classes of SynHandlerBase.
- In use, the SynChan sits on the compartment connected to it by the **channel** message. One or more of the SynHandler objects connects to the SynChan through the **activation** message. The SynHandlers each manage multiple synapses, and the handlers can be fixed weight or have a learning rule.
-
- .. py:method:: setTau1
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTau1
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTau2
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTau2
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNormalizeWeights
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNormalizeWeights
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: activation
-
- (*destination message field*) Sometimes we want to continuously activate the channel
-
-
- .. py:method:: modulator
-
- (*destination message field*) Modulate channel response
-
-
- .. py:attribute:: tau1
-
- double (*value field*) Decay time constant for the synaptic conductance, tau1 >= tau2.
-
-
- .. py:attribute:: tau2
-
- double (*value field*) Rise time constant for the synaptic conductance, tau1 >= tau2.
-
-
- .. py:attribute:: normalizeWeights
-
- bool (*value field*) Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.
-
-
-.. py:class:: SynHandlerBase
-
- Base class for handling synapse arrays converging onto a given channel or integrate-and-fire neuron. This class provides the interface for channels/intFires to connect to a range of synapse types, including simple synapses, synapses with different plasticity rules, and variants yet to be implemented.
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared Finfo to receive Process messages from the clock.
-
-
- .. py:method:: setNumSynapses
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getNumSynapses
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setNumSynapse
-
- (*destination message field*) Assigns number of field entries in field array.
-
-
- .. py:method:: getNumSynapse
-
- (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles 'process' call. Checks if any spike events are due forhandling at this timestep, and does learning rule stuff if needed
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles 'reinit' call. Initializes all the synapses.
-
-
- .. py:attribute:: activationOut
-
- double (*source message field*) Sends out level of activation on all synapses converging to this SynHandler
-
-
- .. py:attribute:: numSynapses
-
- unsigned int (*value field*) Number of synapses on SynHandler. Duplicate field for num\_synapse
-
-
-.. py:class:: Synapse
-
- Synapse using ring buffer for events.
-
- .. py:method:: setWeight
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getWeight
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setDelay
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getDelay
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: addSpike
-
- (*destination message field*) Handles arriving spike messages, inserts into event queue.
-
-
- .. py:attribute:: weight
-
- double (*value field*) Synaptic weight
-
-
- .. py:attribute:: delay
-
- double (*value field*) Axonal propagation delay to this synapse
-
-
-.. py:class:: Table
-
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setThreshold
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getThreshold
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: input
-
- (*destination message field*) Fills data into table. Also handles data sent back following request
-
-
- .. py:method:: spike
-
- (*destination message field*) Fills spike timings into the Table. Signal has to exceed thresh
-
-
- .. py:method:: process
-
- (*destination message field*) Handles process call, updates internal time stamp.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call.
-
-
- .. py:attribute:: requestOut
-
- PSt6vectorIdSaIdEE (*source message field*) Sends request for a field to target object
-
-
- .. py:attribute:: threshold
-
- double (*value field*) threshold used when Table acts as a buffer for spikes
-
-
-.. py:class:: TableBase
-
-
- .. py:method:: setVector
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getVector
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getOutputValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSize
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getY
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: linearTransform
-
- (*destination message field*) Linearly scales and offsets data. Scale first, then offset.
-
-
- .. py:method:: xplot
-
- (*destination message field*) Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname
-
-
- .. py:method:: plainPlot
-
- (*destination message field*) Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename
-
-
- .. py:method:: loadCSV
-
- (*destination message field*) Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator
-
-
- .. py:method:: loadXplot
-
- (*destination message field*) Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.
-
-
- .. py:method:: loadXplotRange
-
- (*destination message field*) Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.
-
-
- .. py:method:: compareXplot
-
- (*destination message field*) Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison\_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
-
-
- .. py:method:: compareVec
-
- (*destination message field*) Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison\_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
-
-
- .. py:method:: clearVec
-
- (*destination message field*) Handles request to clear the data vector
-
-
- .. py:attribute:: vector
-
- vector<double> (*value field*) vector with all table entries
-
-
- .. py:attribute:: outputValue
-
- double (*value field*) Output value holding current table entry or output of a calculation
-
-
- .. py:attribute:: size
-
- unsigned int (*value field*) size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest
-
-
- .. py:attribute:: y
-
- unsigned int,double (*lookup field*) Value of table at specified index
-
-
-.. py:class:: TimeTable
-
- TimeTable: Read in spike times from file and send out eventOut messages
- at the specified times.
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message for process and reinit
-
-
- .. py:method:: setFilename
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getFilename
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMethod
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMethod
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getState
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: process
-
- (*destination message field*) Handle process call
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles reinit call
-
-
- .. py:attribute:: eventOut
-
- double (*source message field*) Sends out spike time if it falls in current timestep.
-
-
- .. py:attribute:: filename
-
- string (*value field*) File to read lookup data from. The file should be contain two columns
- separated by any space character.
-
-
- .. py:attribute:: method
-
- int (*value field*) Method to use for filling up the entries. Currently only method 4
- (loading from file) is supported.
-
-
- .. py:attribute:: state
-
- double (*value field*) Current state of the time table.
-
-
-.. py:class:: VClamp
-
- Voltage clamp object for holding neuronal compartments at a specific voltage.
- This implementation uses a builtin RC circuit to filter the command input and then use a PID to bring the sensed voltage (Vm from compartment) to the filtered command potential.
- Usage: Connect the `currentOut` source of VClamp to `injectMsg` dest of Compartment. Connect the `VmOut` source of Compartment to `set\_sensed` dest of VClamp. Either set `command` field to a fixed value, or connect an appropriate source of command potential (like the `outputOut` message of an appropriately configured PulseGen) to `set\_command` dest.
- The default settings for the RC filter and PID controller should be fine. For step change in command voltage, good defaults withintegration time step dt are as follows:
- time constant of RC filter, tau = 5 * dt
- proportional gain of PID, gain = Cm/dt where Cm is the membrane capacitance of the compartment
- integration time of PID, ti = dt
- derivative time of PID, td = 0
-
- .. py:attribute:: proc
-
- void (*shared message field*) Shared message to receive Process messages from the scheduler
-
-
- .. py:method:: getCommand
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getCurrent
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getSensed
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setMode
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getMode
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTi
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTi
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTd
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTd
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTau
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTau
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setGain
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getGain
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: sensedIn
-
- (*destination message field*) The `VmOut` message of the Compartment object should be connected here.
-
-
- .. py:method:: commandIn
-
- (*destination message field*) The command voltage source should be connected to this.
-
-
- .. py:method:: process
-
- (*destination message field*) Handles 'process' call on each time step.
-
-
- .. py:method:: reinit
-
- (*destination message field*) Handles 'reinit' call
-
-
- .. py:attribute:: currentOut
-
- double (*source message field*) Sends out current output of the clamping circuit. This should be connected to the `injectMsg` field of a compartment to voltage clamp it.
-
-
- .. py:attribute:: command
-
- double (*value field*) Command input received by the clamp circuit.
-
-
- .. py:attribute:: current
-
- double (*value field*) The amount of current injected by the clamp into the membrane.
-
-
- .. py:attribute:: sensed
-
- double (*value field*) Membrane potential read from compartment.
-
-
- .. py:attribute:: mode
-
- unsigned int (*value field*) Working mode of the PID controller.
-
- mode = 0, standard PID with proportional, integral and derivative all acting on the error.
-
- mode = 1, derivative action based on command input
-
- mode = 2, proportional action and derivative action are based on command input.
-
-
- .. py:attribute:: ti
-
- double (*value field*) Integration time of the PID controller. Defaults to 1e9, i.e. integral action is negligibly small.
-
-
- .. py:attribute:: td
-
- double (*value field*) Derivative time of the PID controller. This defaults to 0,i.e. derivative action is unused.
-
-
- .. py:attribute:: tau
-
- double (*value field*) Time constant of the lowpass filter at input of the PID controller. This smooths out abrupt changes in the input. Set it to 5 * dt or more to avoid overshoots.
-
-
- .. py:attribute:: gain
-
- double (*value field*) Proportional gain of the PID controller.
-
-
-.. py:class:: Variable
-
- Variable for storing double values. This is used in Function class.
-
- .. py:method:: setValue
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getValue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setVar
-
- (*destination message field*) Handles incoming variable value.
-
-
- .. py:attribute:: value
-
- double (*value field*) Variable value
-
-
-.. py:class:: VectorTable
-
-
- .. py:method:: setXdivs
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXdivs
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXmin
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmin
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setXmax
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getXmax
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getInvdx
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: setTable
-
- (*destination message field*) Assigns field value.
-
-
- .. py:method:: getTable
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getLookupvalue
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:method:: getLookupindex
-
- (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value.
-
-
- .. py:attribute:: xdivs
-
- unsigned int (*value field*) Number of divisions.
-
-
- .. py:attribute:: xmin
-
- double (*value field*) Minimum value in table.
-
-
- .. py:attribute:: xmax
-
- double (*value field*) Maximum value in table.
-
-
- .. py:attribute:: invdx
-
- double (*value field*) Maximum value in table.
-
-
- .. py:attribute:: table
-
- vector<double> (*value field*) The lookup table.
-
-
- .. py:attribute:: lookupvalue
-
- double,double (*lookup field*) Lookup function that performs interpolation to return a value.
-
-
- .. py:attribute:: lookupindex
-
- unsigned int,double (*lookup field*) Lookup function that returns value by index.
-
-
-.. py:class:: ZombieBufPool
-
-
-.. py:class:: ZombieCaConc
-
- ZombieCaConc: Calcium concentration pool. Takes current from a channel and keeps track of calcium buildup and depletion by a single exponential process.
-
-.. py:class:: ZombieCompartment
-
- Compartment object, for branching neuron models.
-
-.. py:class:: ZombieEnz
-
-
-.. py:class:: ZombieFuncPool
-
-
- .. py:method:: input
-
- (*destination message field*) Handles input to control value of n\_
-
-
-.. py:class:: ZombieHHChannel
-
- ZombieHHChannel: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.
-
-.. py:class:: ZombieMMenz
-
-
-.. py:class:: ZombiePool
-
-
-.. py:class:: ZombieReac
-
-
-.. py:class:: testSched
-
-
- .. py:method:: process
-
- (*destination message field*) handles process call
-
-
diff --git a/moose-core/Docs/user/py/moose_cookbook.rst b/moose-core/Docs/user/py/moose_cookbook.rst
deleted file mode 100644
index de31923895cfefeb9eecc6f415488c2ddfdd7809..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/moose_cookbook.rst
+++ /dev/null
@@ -1,688 +0,0 @@
-.. A cookbook for MOOSE
-.. Lists all the snippets in moose-examples/snippets directory
-
-MOOSE Cookbook
-==============
-
-The MOOSE Cookbook contains recipes showing you how to do specific
-tasks in MOOSE.
-
-Loading and running models
---------------------------
-This section of the documentation explains how to load and run predefined
-models in MOOSE.
-
-
-Hello, MOOSE: Load, run and display existing models
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: helloMoose
- :members:
-
-.. _squid:
-
-The Hodgkin-Huxley demo
-^^^^^^^^^^^^^^^^^^^^^^^
-This is a self-contained graphical demo implemented by Subhasis Ray,
-closely based on the 'Squid' demo by Mark Nelson which ran in GENESIS.
-
-.. figure:: ../../images/squid_demo.png
- :alt: Hodgkin-Huxley's squid giant axon experiment
-
- Simulation of Hodgkin-Huxley's experiment on squid giant axon
- showing action potentials generated by a step current injection.
-
-
-The demo has built-in documentation and may be run from the
-``moose-examples/squid`` subdirectory of MOOSE. If you want to read a simpler
-implementation of the same (without the code for setting up GUI),
-check out :ref:`hhmodel`.
-
-Start, Stop, and setting clocks
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: startstop
- :members:
-
-Run Python from MOOSE
-^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: pyrun
- :members:
-
-Accessing and tweaking parameters
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: tweakingParameters
- :members:
-.. figure:: ../../images/tweakingParameters.png
- :alt: Three oscillation patterns after tweaking model parameters.
-
-Storing simulation output
-^^^^^^^^^^^^^^^^^^^^^^^^^
-Here we'll show how to store and dump from a table and also using HDF5.
-
-.. automodule:: tabledemo
- :members:
-
-.. automodule:: hdfdemo
- :members:
-
-.. automodule:: nsdf
- :members:
-
-Computing arbitrary functions on the fly
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Sometimes you want to calculate arbitrary function of the state
-variables of one or more elements and feed the result into another
-element during a simulation. The Function class is useful for this.
-
-.. figure:: ../../images/function.png
- :alt: Outputs of Function object calculating z = c0 * exp(c1 * x) * cos(y)
- :scale: 50%
-
-
-.. automodule:: function
- :members:
-
-Solving arbitrary differential equations
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-The Function classes are also useful for setting up arbitrary differential
-equations. MOOSE supports solution of such equation systems, with the
-caveat that it thinks they should be chemical systems and therefore
-interprets the variables as concentrations. MOOSE does not permit the
-concentrations to go negative.
-
-.. automodule:: diffEqSolution
- :members:
-
-This limitation on positive solutions can be overcome with offsets to the
-variables.
-
-.. automodule:: funcRateHarmonicOsc
- :members:
-
-It is also possible to set up other forms of differential equations,
-where instead of directly controlling the rate of change of a pool, the
-equations take the form of modifying the rate of a reaction involving
-a pool.
-
-.. automodule:: funcReacLotkaVolterra
- :members:
-
-The solutions of such systems are much more accurate and faster using the
-chemical kinetic solver than with the basic exponential Euler method.
-However, it is important to point out that the use of arbitrary
-differential equations to represent chemical systems is
-discouraged in MOOSE. This is for the simple reason that they are
-abstractions, frequently with serious flaws, of the underlying chemistry.
-At the current time the stochastic solver cannot handle systems formulated
-with functions rather than chemical objects.
-
-Chemical Signaling models
--------------------------
-This section of the documentation explains how to do operations specific
-to the chemical signaling.
-
-Running with different numerical methods
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: switchKineticSolvers
- :members:
-
-Changing volumes
-^^^^^^^^^^^^^^^^
-.. automodule:: scaleVolumes
- :members:
-
-Feeding tabulated input to a model
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: analogStimTable
- :members:
-
-Finding steady states
-^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: findChemSteadyState
- :members:
-
-Making a dose-response curve
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. figure:: ../../images/chemDoseResponse.png
- :alt: Dose-response curve example for a bistable system.
-.. automodule:: chemDoseResponse
- :members:
-
-Building a chemical model from parts
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Disclaimer: Avoid doing this for all but the very simplest models. This
-is error-prone, tedious, and non-portable. For preference use one of the
-standard model formats like SBML, which MOOSE and many other tools can
-read and write.
-
-Nevertheless, it is useful to see how these models are set up.
-There are several tutorials and snippets that build the entire chemical
-model system using the basic MOOSE calls. The sequence of steps is
-typically:
-
- #. Create container (chemical compartment) for model. This is typically
- a CubeMesh, a CylMesh, and if you really know what you are doing,
- a NeuroMesh.
- #. Create the reaction components: pools of molecules **moose.Pool**;
- reactions **moose.Reac**; and enzymes **moose.Enz**. Note that when
- creating an enzyme, one must also create a molecule beneath it to
- serve as the enzyme-substrate complex. Other less-used
- components include Michaelis-Menten enzymes **moose.MMenz**, input
- tables, pulse generators and so on. These are illustrated in other
- examples. All these reaction components should be child objects
- of the compartment, since this defines what volume they will occupy.
- Specifically , a pool or reaction object must be placed somewhere
- below the compartment in the object tree for the volume to be
- set correctly and for the solvers to know what to use.
- #. Assign parameters for the components.
-
- * Compartments have a **volume**, and each subtype will have
- quite elaborate options for partitioning the compartment
- into voxels.
- * **Pool** s have one key parameter, the initial
- concentration **concInit**.
- * **Reac** tions have two parameters: **Kf** and **Kb**.
- * **Enz** ymes have two primary parameters **kcat** and **Km**.
- That is enough for **MMenz** ymes. Regular **Enz** ymes have
- an additional parameter **k2** which by default is set to 4.0
- times **kcat**, but you may also wish to explicitly assign it
- if you know its value.
-
- #. Connect up the reaction system using moose messaging.
- #. Create and connect up input and output tables as needed.
- #. Create and connect up the solvers as needed. This has to be done
- in a specific order. Examples are linked below, but briefly the
- order is:
-
- a. Make the compartment and reaction system.
- b. Make the Ksolve or Gsolve.
- c. Make the Stoich.
- d. Assign **stoich.compartment** to the compartment
- e. Assign **stoich.ksolve** to either the Ksolve or Gsolve.
- f. Assign **stoich.path** to finally fill in the reaction system.
-
- There is an additional step if diffusion is also present, see
- `Reaction-diffusion in a cylinder`_.
-
-Some examples of doing this are in:
-
- * `Making a dose-response curve`_ , which defines a small bistable
- system including three **Pool** s, two **Enz** ymes and a
- **Reac** tion.
- * `Feeding tabulated input to a model`_, which shows how to connect up
- a **StimulusTable** object to a simple 2-molecule reaction.
- * `Reaction-diffusion in a cylinder`_, which defines a simple binding
- reaction and embeds it in a 1-dimensional diffusive volume of
- a cylinder.
-
-The recommended way to build a chemical model, of course, is to load it
-in from a file format specific to such models. MOOSE understands
-**SBML**, **kkit.g** (a legacy GENESIS format), and **cspace**
-(a very compact format used in a large study of bistables from
-Ramakrishnan and Bhalla, PLoS Comp. Biol 2008).
-
-One key concept is that in MOOSE the components, messaging, and access
-to model components is identical regardless of whether the model was
-built from parts, or loaded in from a file. All that the file loaders do
-is to use the file to automate the steps above. Thus the model components
-and their fields are completely accessible from the script even if
-the model has been loaded from a file. See
-`Accessing and tweaking parameters`_ for an example of this.
-
-
-Oscillation models
-^^^^^^^^^^^^^^^^^^
-There are several chemical oscillators defined in the
-``moose-examples/tutorials/ChemkcalOscillators`` directory. These include:
-
-1. Slow Feedback Oscillator based on a model by Boris Kholdenko
-
-.. automodule:: slowFbOsc
- :members:
-
-2. Repressilator, based on Elowitz and Liebler, Nature 2000.
-
-.. automodule:: repressillator
- :members:
-
-3. Relaxation oscillator.
-
-.. automodule:: relaxationOsc
- :members:
-
-
-Bistability models
-^^^^^^^^^^^^^^^^^^
-There are several bistable models defined in the
-``moose-examples/tutorials/ChemkcalBistables`` directory. These include:
-
-1. MAPK feedback loop model.
-
-.. automodule:: mapkFB
- :members:
-
-2. Simple minimal bistable model, run stochastically at different volumes
- to illustrate the effects of chemical noise.
-
-.. automodule:: scaleVolumes
- :members:
-
-3. Strongly bistable model.
-
-.. automodule:: strongBis
- :members:
-
-Reaction-diffusion models
--------------------------
-The MOOSE design for reaction-diffusion is to specify one or
-more cellular 'compartments', and embed reaction systems in each of them.
-
-A 'compartment', in the context of reaction-diffusion, is used in the
-cellular sense of a biochemically defined,
-volume restricted subpart of a cell. Many but not all compartments
-are bounded by a cell membrane, but biochemically the membrane itself
-may form a compartment. Note that this interpretation differs from that
-of a 'compartment' in detailed electrical models of neurons.
-
-A reaction system can be loaded in from any of the supported MOOSE
-formats, or built within Python from MOOSE parts.
-
-The computations for such models are done by a set of objects:
-Stoich, Ksolve and Dsolve. Respectively, these handle the model
-reactions and stoichiometry matrix, the reaction computations for
-each voxel, and the diffusion between voxels. The 'Compartment' specifies
-how the model should be spatially discretized.
-
-Reaction-diffusion + transport in a tapering cylinder
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: cylinderDiffusion
- :members:
-
-A Turing model
-^^^^^^^^^^^^^^
-.. automodule:: TuringOneDim
- :members:
-
-A spatial bistable model
-^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: propagationBis
-
-Reaction-diffusion in neurons
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Reaction-diffusion systems can easily be embedded into neuronal geometries.
-MOOSE does so by treating each neuron as a pseudo 1-dimensional object.
-This means that diffusion only happens along the axis of dendritic
-segments, not radially from inside to outside a dendrite, nor tangentially
-around the dendrite circumference.
-Here we illustrate two cases. The simple case treats the entire neuron
-as a single, chemically equivalent reaction-diffusion system in a binary
-branching neuronal tree. The more complex example shows how to set up
-three chemically distinct kinds of subdivisions within the neuron:
-the dendritic tree, the dendritic spine heads, and the postsynaptic
-densities. In both examples we embed a simple Turing-like spatial oscillator
-in every compartment of the model neurons, so as to see nice oscillations
-and animations. The first example has a particularly striking pseudo-3D
-rendition of the neuron and the molecular spatial oscillations within it.
-
-.. figure:: ../../images/reacDiffBranchingNeuron.png
- :alt: Pseudo-3-D rendition of branching neuron and the concs in it.
-
-.. automodule:: reacDiffBranchingNeuron
- :members:
-.. automodule:: reacDiffSpinyNeuron
- :members:
-
-Transport in branching dendritic tree
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: transportBranchingNeuron
- :members:
-
-Cross-compartment reaction systems
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Frequently reaction systems span cellular (chemical) compartments.
-For example, a membrane-bound molecule may be phosphorylated by a
-cytosolic kinase, using soluble ATP as one of the substrates. Here the
-membrane and the cytsol are different chemical compartments.
-MOOSE supports such reactions. The following snippets illustrate
-cross-compartment chemistry. Note that the interpretation of the rates
-of enzymes and reactions does depend on which compartment they reside in.
-
-.. automodule:: crossComptSimpleReac
- :members:
-.. automodule:: crossComptOscillator
- :members:
-.. automodule:: crossComptNeuroMesh
- :members:
-
-Single neuron models
---------------------
-
-Neurons are modelled as equivalent electrical circuits. The morphology
-of a neuron can be broken into isopotential compartments connected by
-axial resistances R\ :sub:`a`\ denoting the cytoplasmic
-resistance. In each compartment, the neuronal membrane is represented as
-a capacitance C\ :sub:`m`\ with a shunt leak resistance
-R\ :sub:`m`\ . Electrochemical gradient (due to ion pumps)
-across the leaky membrane causes a voltage drive E\ :sub:`m`\ ,
-that hyperpolarizes the inside of the cell membrane compared to the
-outside.
-
-Each voltage dependent ion channel, present on the membrane, is modelled
-as a voltage dependent conductance G\ :sub:`k`\ with gating
-kinetics, in series with an electrochemical voltage drive (battery)
-E\ :sub:`k`\ , across the membrane capacitance
-C\ :sub:`m`\ , as in the figure below.
-
---------------
-
-.. figure:: ../../images/neuroncompartment.png
- :align: center
- :alt: **Equivalent circuit of neuronal compartments**
-
- **Equivalent circuit of neuronal compartments**
-
---------------
-
-Neurons fire action potentials / spikes (sharp rise and fall of membrane
-potential V\ :sub:`m`\ ) due to voltage dependent channels.
-These result in opening of excitatory / inhibitory synaptic channels
-(conductances with batteries, similar to voltage gated channels) on
-other connected neurons in the network.
-
-MOOSE can handle large networks of detailed neurons, each with
-complicated channel dynamics. Further, MOOSE can integrate chemical
-signalling with electrical activity. Presently, creating and simulating
-these requires PyMOOSE scripting, but these will be incorporated into
-the GUI in the future.
-
-To understand channel kinetics and neuronal action potentials, run the
-Squid Axon demo installed along with MOOSEGUI and consult its
-help/tutorial.
-
-Read more about compartmental modelling in the first few chapters of the
-`Book of
-Genesis <http://www.genesis-sim.org/GENESIS/iBoG/iBoGpdf/index.html>`_.
-
-Models can be defined in `NeuroML <http://www.neuroml.org>`_, an XML
-format which is mostly supported across simulators. Channels, neuronal
-morphology (compartments), and networks can be specified using various
-levels of NeuroML, namely ChannelML, MorphML and NetworkML. Importing of
-cell models in the `GENESIS <http://www.genesis-sim.org/GENESIS>`_
-.p format is supported for backwards compatibitility.
-
-Modeling details
-^^^^^^^^^^^^^^^^^
-
-Some salient properties of neuronal building blocks in MOOSE are
-described below. Variables that are updated at every simulation time
-step are are listed **dynamical**. Rest are parameters.
-
-- **Compartment**
- When you select a compartment, you can view and edit its properties
- in the right pane. V\ :sub:`m`\ and I\ :sub:`m`\
- are plot-able.
-
- - V\ :sub:`m`\
- membrane potential (across C\ :sub:`m`\ ) in Volts. It is a
- dynamical variable.
- - C\ :sub:`m`\
- membrane capacitance in Farads.
- - E\ :sub:`m`\
- membrane leak potential in Volts due
- to the electrochemical gradient setup by ion pumps.
- - I\ :sub:`m`\
- current in Amperes across the membrane via leak resistance R\
- :sub:`m`\ .
- - inject
- current in Amperes injected externally into the compartment.
- - initVm
- initial V\ :sub:`m`\ in Volts.
- - R\ :sub:`m`\
- membrane leak resistance in Ohms due to leaky channels.
- - diameter
- diameter of the compartment in metres.
- - length
- length of the compartment in metres.
-
-- **HHChannel**
- Hodgkin-Huxley channel with voltage dependent dynamical gates.
-
- - Gbar
- peak channel conductance in Siemens.
- - E\ :sub:`k`\
- reversal potential of the channel, due to electrochemical
- gradient of the ion(s) it allows.
- - G\ :sub:`k`\
- conductance of the channel in Siemens.
- G\ :sub:`k`\ (t) = Gbar × X(t)\ :sup:`Xpower`\ ×
- Y(t)\ :sup:`Ypower`\ × Z(t)\ :sup:`Zpower`\
-
- - I\ :sub:`k`\
- current through the channel into the neuron in Amperes.
- I\ :sub:`k`\ (t) = G\ :sub:`k`\ (t) ×
- (E\ :sub:`k`\ -V\ :sub:`m`\ (t))
-
- - X, Y, Z
- gating variables (range 0.0 to 1.0) that may turn on or off as
- voltage increases with different time constants.
-
- dX(t)/dt = X\ :sub:`inf`\ /Ï„ - X(t)/Ï„
-
- Here, X\ :sub:`inf`\ and Ï„ are typically
- sigmoidal/linear/linear-sigmoidal functions of membrane
- potential V\ :sub:`m`\ , which are described in a ChannelML
- file and presently not editable from MOOSEGUI. Thus, a gate
- may open (X\ :sub:`inf`\ (V\ :sub:`m`\ ) → 1) or close (X\
- :sub:`inf`\ (V\ :sub:`m`\ ) → 0) on increasing V\ :sub:`m`\
- , with time constant Ï„(V\ :sub:`m`\ ).
-
- - Xpower, Ypower, Zpower
- powers to which gates are raised in the G\ :sub:`k`\ (t)
- formula above.
-
-- **HHChannel2D**
- The Hodgkin-Huxley channel2D can have the usual voltage dependent
- dynamical gates, and also gates that depend on voltage and an
- ionic concentration, as for say Ca-dependent K conductance. It has
- the properties of HHChannel above, and a few more, similar to
- in the `GENESIS tab2Dchannel
- reference <http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-26.html#ss26.61>`_.
-
-- **CaConc**
- This is a pool of Ca ions in each compartment, in a shell volume
- under the cell membrane. The dynamical Ca concentration increases
- when Ca channels open, and decays back to resting with a specified
- time constant Ï„. Its concentration controls Ca-dependent K channels,
- etc.
-
- - Ca
- Ca concentration in the pool in units mM ( i.e., mol/m\
- :sup:`3`\ ).
-
- d[Ca\ :sup:`2+`\ ]/dt = B × I\ :sub:`Ca`\ -
- [Ca\ :sup:`2+`\ ]/Ï„
-
- - CaBasal/Ca_base
- Base Ca concentration to which the Ca decays
- - tau
- time constant with which the Ca concentration decays to the base Ca level.
- - B
- constant in the [Ca\ :sup:`2+`\ ] equation above.
- - thick
- thickness of the Ca shell within the cell membrane which is
- used to calculate B (see Chapter 19 of `Book of GENESIS
- <http://www.genesis-sim.org/GENESIS/iBoG/iBoGpdf/index.html>`_.)
-
-Neuronal simulations in MOOSEGUI
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Neuronal models in various formats can be loaded and simulated in the
-**MOOSE Graphical User Interface**. The GUI displays the neurons in 3D,
-and allows visual selection and editing of neuronal properties. Plotting
-and visualization of activity proceeds concurrently with the simulation.
-Support for creating and editing channels, morphology and networks is
-planned for the future. MOOSEGUI uses SI units throughout.
-
-moose-examples
-^^^^^^^^^^^^^^^
-
-- **Cerebellar granule cell**
-
- **File -> Load ->**
- ~/moose/moose-examples/neuroml/GranuleCell/GranuleCell.net.xml
-
- This is a single compartment Cerebellar granule cell with a variety
- of channels `Maex, R. and De Schutter, E.,
- 1997 <http://www.tnb.ua.ac.be/models/network.shtml>`_ (exported from
- http://www.neuroconstruct.org/). Click on its soma, and **See
- children** for its list of channels. Vary the Gbar of these
- channels to obtain regular firing, adapting and bursty behaviour (may
- need to increase tau of the Ca pool).
-
-
-- **Pyloric rhythm generator in the stomatogastric ganglion of lobster**
-
- **File -> Load ->**
- ~/moose/moose-examples/neuroml/pyloric/Generated.net.xml
-
-
-- **Purkinje cell**
-
- **File -> Load ->**
- ~/moose/moose-examples/neuroml/PurkinjeCell/Purkinje.net.xml
-
- This is a purely passive cell, but with extensive morphology [De
- Schutter, E. and Bower, J. M., 1994] (exported from
- http://www.neuroconstruct.org/). The channel specifications are in an
- obsolete ChannelML format which MOOSE does not support.
-
-
-- **Olfactory bulb subnetwork**
-
- **File -> Load ->**
- ~/moose/moose-examples/neuroml/OlfactoryBulb/numgloms2_seed100.0_decimated.xml
-
- This is a pruned and decimated version of a detailed network model
- of the Olfactory bulb [Gilra A. and Bhalla U., in preparation]
- without channels and synaptic connections. We hope to post the
- ChannelML specifications of the channels and synapses soon.
-
-
-- **All channels cell**
-
- **File -> Load ->**
- ~/moose/moose-examples/neuroml/allChannelsCell/allChannelsCell.net.xml
-
- This is the Cerebellar granule cell as above, but with loads of
- channels from various cell types (exported from
- http://www.neuroconstruct.org/). Play around with the channel
- properties to see what they do. You can also edit the ChannelML files
- in ~/moose/moose-examples/neuroml/allChannelsCell/cells_channels/ to
- experiment further.
-
-
-- **NeuroML python scripts**
- In directory ~/moose/moose-examples/neuroml/GranuleCell, you can run
- python FvsI_Granule98.py which plots firing rate vs injected
- current for the granule cell. Consult this python script to see how
- to read in a NeuroML model and to set up simulations. There are ample
- snippets in ~/moose/moose-examples/snippets too.
-
-Loading, modifying, saving
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-Explicit vs. implict methods
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Integrate-and-fire models
-^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: IntegrateFireZoo
- :members:
-
-The HH model
-^^^^^^^^^^^^
-.. _hhmodel:
-
-This is a standalone script for simulating the Hodgkin-Huxley squid
-axon experiment with a step current injection. The graphical version
-of the same is :ref:`squid`.
-
-.. automodule:: ionchannel
- :members:
-
-Analyzing spike trains
-^^^^^^^^^^^^^^^^^^^^^^
-
-Network models
---------------
-Connecting two cells via a synapse
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Below is the connectivity diagram for setting up a synaptic connection
-from one neuron to another. The PulseGen object is there for
-stimulating the presynaptic cell as part of experimental setup. The
-cells are defined as single-compartments with Hodgkin-Huxley type Na+
-and K+ channels (see :ref:`hhmodel`)
-
-.. figure:: ../../images/twoCells.png
- :scale: 50%
- :alt: Two cells connected via synapse
-
-.. automodule:: twocells
- :members:
-
-Plastic synapse: STDP
-^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: STDP
- :members:
-
-Network with Ca-based plasticity
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: ExcInhNet_HigginsGraupnerBrunel2014
- :members:
-
-Providing random input to a cell
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: randomspike
- :members:
-
-.. figure:: ../../images/randomSpike.png
- :scale: 50%
- :alt: Random spike input to a cell
-
-Recurrent integrate-and-fire network
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: ExcInhNet_Ostojic2014_Brunel2000
- :members:
-
-Recurrent integrate-and-fire network with plasticity
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-A feed-forward network with random input
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Using compartmental models in networks
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-**Pyloric rhythm generator in the stomatogastric ganglion of lobster**
-
-.. automodule:: STG_net
- :members:
-
-Multiscale models
------------------
-Single-compartment multiscale model
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: multiscaleOneCompt
- :members:
-
-Multi-compartment multiscale model
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Graphics
---------
-Displaying time-series plots
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Animation of values along an axis
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Using MOOGLI widgets to display a neuron
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-
diff --git a/moose-core/Docs/user/py/moose_quickstart.rst b/moose-core/Docs/user/py/moose_quickstart.rst
deleted file mode 100644
index d5468d2c6478216831dacf21c1d64b62e6a3ad6d..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/py/moose_quickstart.rst
+++ /dev/null
@@ -1,684 +0,0 @@
-***********************************************
-Getting started with python scripting for MOOSE
-***********************************************
-
-.. :Author: Subhasis Ray
-.. :Date: December 12, 2012,
-.. :Last-Updated: Jan 21, 2016
-.. :By: Harsha Rani
-
-.. _quickstart-intro:
-
-Introduction
-============
-
-This document describes how to use the ``moose`` module in Python
-scripts or in an interactive Python shell. It aims to give you enough
-overview to help you start scripting using MOOSE and extract farther
-information that may be required for advanced work. Knowledge of
-Python or programming in general will be helpful. If you just want to
-simulate existing models in one of the supported formats, you can fire
-the MOOSE GUI and locate the model file using the ``File`` menu and
-load it. The GUI is described in separate document. If you
-are looking for recipes for specific tasks, take a look at
-:doc:`moose_cookbook`. The example code in the boxes can be entered in
-a Python shell.
-
-.. _quickstart-importing:
-
-Importing MOOSE and accessing built-in documentation
-====================================================
-
-In a python script you import modules to access the functionalities they
-provide. ::
-
- >>> import moose
-
-This makes the ``moose`` module available for use in Python. You can use
-Python's built-in ``help`` function to read the top-level documentation
-for the moose module ::
-
- >>> help(moose)
-
-This will give you an overview of the module. Press ``q`` to exit the
-pager and get back to the interpreter. You can also access the
-documentation for individual classes and functions this way. ::
-
- >>> help(moose.connect)
-
-To list the available functions and classes you can use ``dir``
-function [1]_. ::
-
- >>> dir(moose)
-
-MOOSE has built-in documentation in the C++-source-code independent of
-Python. The ``moose`` module has a separate ``doc`` function to extract
-this documentation. ::
-
- >>> moose.doc(moose.Compartment)
-
-The class level documentation will show whatever the author/maintainer
-of the class wrote for documentation followed by a list of various kinds
-of fields and their data types. This can be very useful in an
-interactive session.
-
-Each field can have its own detailed documentation, too. ::
-
- >>> moose.doc('Compartment.Rm')
-
-Note that you need to put the class-name followed by dot followed by
-field-name within quotes. Otherwise, ``moose.doc`` will receive the
-field value as parameter and get confused.
-
-.. _quickstart-creating:
-Creating objects and traversing the object hierarchy
-----------------------------------------------------
-
-Different types of biological entities like neurons, enzymes, etc are
-represented by classes and individual instances of those types are
-objects of those classes. Objects are the building-blocks of models in
-MOOSE. We call MOOSE objects ``element`` and use object and element
-interchangeably in the context of MOOSE. Elements are conceptually laid
-out in a tree-like hierarchical structure. If you are familiar with file
-system hierarchies in common operating systems, this should be simple.
-
-At the top of the object hierarchy sits the ``Shell``, equivalent to the
-root directory in UNIX-based systems and represented by the path ``/``.
-You can list the existing objects under ``/`` using the ``le`` function. ::
-
- >>> moose.le()
- Elements under /
- /Msgs
- /clock
- /classes
- /postmaster
-
-``Msgs``, ``clock`` and ``classes`` are predefined objects in MOOSE. And
-each object can contain other objects inside them. You can see them by
-passing the path of the parent object to ``le`` ::
-
- >>> moose.le('/Msgs')
- Elements under /Msgs[0]
- /Msgs[0]/singleMsg
- /Msgs[0]/oneToOneMsg
- /Msgs[0]/oneToAllMsg
- /Msgs[0]/diagonalMsg
- /Msgs[0]/sparseMsg
-
-Now let us create some objects of our own. This can be done by invoking
-MOOSE class constructors (just like regular Python classes). ::
-
- >>> model = moose.Neutral('/model')
-
-The above creates a ``Neutral`` object named ``model``. ``Neutral`` is
-the most basic class in MOOSE. A ``Neutral`` element can act as a
-container for other elements. We can create something under ``model`` ::
-
- >>> soma = moose.Compartment('/model/soma')
-
-Every element has a unique path. This is a concatenation of the names of
-all the objects one has to traverse starting with the root to reach that
-element. ::
-
- >>> print soma.path
- /model/soma
-
-The name of the element can be printed, too. ::
-
- >>> print soma.name
- soma
-
-The ``Compartment`` elements model small sections of a neuron. Some
-basic experiments can be carried out using a single compartment. Let us
-create another object to act on the ``soma``. This will be a step
-current generator to inject a current pulse into the soma. ::
-
- >>> pulse = moose.PulseGen('/model/pulse')
-
-You can use ``le`` at any point to see what is there ::
-
- >>> moose.le('/model')
- Elements under /model
- /model/soma
- /model/pulse
-
-And finally, we can create a ``Table`` to record the time series of the
-soma's membrane potential. It is good practice to organize the data
-separately from the model. So we do it as below ::
-
- >>> data = moose.Neutral('/data')
- >>> vmtab = moose.Table('/data/soma_Vm')
-
-Now that we have the essential elements for a small model, we can go on
-to set the properties of this model and the experimental protocol.
-
-.. _quickstart-properties:
-
-Setting the properties of elements: accessing fields
-====================================================
-
-Elements have several kinds of fields. The simplest ones are the
-``value fields``. These can be accessed like ordinary Python members.
-You can list the available value fields using ``getFieldNames``
-function ::
-
- >>> soma.getFieldNames('valueFinfo')
-
-Here ``valueFinfo`` is the type name for value fields. ``Finfo`` is
-short form of *field information*. For each type of field there is a
-name ending with ``-Finfo``. The above will display the following
-list ::
-
- ('this',
- 'name',
- 'me',
- 'parent',
- 'children',
- 'path',
- 'class',
- 'linearSize',
- 'objectDimensions',
- 'lastDimension',
- 'localNumField',
- 'pathIndices',
- 'msgOut',
- 'msgIn',
- 'Vm',
- 'Cm',
- 'Em',
- 'Im',
- 'inject',
- 'initVm',
- 'Rm',
- 'Ra',
- 'diameter',
- 'length',
- 'x0',
- 'y0',
- 'z0',
- 'x',
- 'y',
- 'z')
-
-Some of these fields are for internal or advanced use, some give access
-to the physical properties of the biological entity we are trying to
-model. Now we are interested in ``Cm``, ``Rm``, ``Em`` and ``initVm``.
-In the most basic form, a neuronal compartment acts like a parallel
-``RC`` circuit with a battery attached. Here ``R`` and ``C`` are
-resistor and capacitor connected in parallel, and the battery with
-voltage ``Em`` is in series with the resistor, as shown below:
-
-
-
-.. figure:: ../../images/neuronalcompartment.jpg
- :alt: **Passive neuronal compartment**
-
- **Passive neuronal compartment**
-
-
-
-The fields are populated with some defaults. ::
-
- >>> print soma.Cm, soma.Rm, soma.Vm, soma.Em, soma.initVm
- 1.0 1.0 -0.06 -0.06 -0.06
-
-
-You can set the ``Cm`` and ``Rm`` fields to something realistic using
-simple assignment (we follow SI unit) [2]_. ::
-
- >>> soma.Cm = 1e-9
- >>> soma.Rm = 1e7
- >>> soma.initVm = -0.07
-
-Instead of writing print statements for each field, you could use the
-utility function showfield to see that the changes took effect ::
-
- >>> moose.showfield(soma)
- [ /soma[0] ]
- diameter = 0.0
- Ra = 1.0
- y0 = 0.0
- Rm = 10000000.0
- numData = 1
- inject = 0.0
- initVm = -0.07
- Em = -0.06
- y = 0.0
- numField = 1
- path = /soma[0]
- dt = 5e-05
- tick = 4
- z0 = 0.0
- name = soma
- Cm = 1e-09
- x0 = 0.0
- Vm = -0.06
- className = Compartment
- length = 0.0
- Im = 0.0
- x = 0.0
- z = 0.0
-
-Now we can setup the current pulse to be delivered to the soma ::
-
- >>> pulse.delay[0] = 50e-3
- >>> pulse.width[0] = 100e-3
- >>> pulse.level[0] = 1e-9
- >>> pulse.delay[1] = 1e9
-
-This tells the pulse generator to create a 100 ms long pulse 50 ms after
-the start of the simulation. The amplitude of the pulse is set to 1 nA.
-We set the delay for the next pulse to a very large value (larger than
-the total simulation time) so that the stimulation stops after the first
-pulse. Had we set ``pulse.delay = 0`` , it would have generated a pulse
-train at 50 ms intervals.
-
-.. _quickstart-connections:
-
-Putting them together: setting up connections
-=============================================
-
-In order for the elements to interact during simulation, we need to
-connect them via messages. Elements are connected to each other using
-special source and destination fields. These types are named
-``srcFinfo`` and ``destFinfo``. You can query the available source and
-destination fields on an element using ``getFieldNames`` as before. This
-time, let us do it another way: by the class name ::
-
- >>> moose.getFieldNames('PulseGen', 'srcFinfo')
- ('childMsg', 'output')
-
-This form has the advantage that you can get information about a class
-without creating elements of that class.
-
-Here ``childMsg`` is a source field that is used by the MOOSE internals
-to connect child elements to parent elements. The second one is of our
-interest. Check out the built-in documentation here ::
-
- >>> moose.doc('PulseGen.output')
- PulseGen.output: double - source field
- Current output level.
-
-so this is the output of the pulse generator and this must be injected
-into the ``soma`` to stimulate it. But where in the ``soma`` can we send
-it? Again, MOOSE has some introspection built in. ::
-
- >>> soma.getFieldNames('destFinfo')
- ('parentMsg',
- 'setThis',
- 'getThis',
- ...
- 'setZ',
- 'getZ',
- 'injectMsg',
- 'randInject',
- 'cable',
- 'process',
- 'reinit',
- 'initProc',
- 'initReinit',
- 'handleChannel',
- 'handleRaxial',
- 'handleAxial')
-
-Now that is a long list. But much of it are fields for internal or
-special use. Anything that starts with ``get`` or ``set`` are internal
-``destFinfo`` used for accessing value fields (we shall use one of those
-when setting up data recording). Among the rest ``injectMsg`` seems to
-be the most likely candidate. Use the ``connect`` function to connect
-the pulse generator output to the soma input ::
-
- >>> m = moose.connect(pulse, 'output', soma, 'injectMsg')
-
-``connect(source, source_field, dest, dest_field)`` creates a
-``message`` from ``source`` element's ``source_field`` field to ``dest``
-elements ``dest_field`` field and returns that message. Messages are
-also elements. You can print them to see their identity ::
-
- >>> print m
- <moose.SingleMsg: id=5, dataId=733, path=/Msgs/singleMsg[733]>
-
-You can print any element as above and the string representation will
-show you the class, two numbers(\ ``id`` and ``dataId``) uniquely
-identifying it among all elements, and its path. You can get some more
-information about a message ::
-
- >>> print m.e1.path, m.e2.path, m.srcFieldsOnE1, m.destFieldsOnE2
- /model/pulse /model/soma ('output',) ('injectMsg',)
-
-
-will confirm what you already know.
-
-
-A message element has fields ``e1`` and ``e2`` referring to the elements
-it connects. For single one-directional messages these are source and
-destination elements, which are ``pulse`` and ``soma`` respectively. The
-next two items are lists of the field names which are connected by this
-message.
-
-You could also check which elements are connected to a particular field ::
-
- >>> print soma.neighbors['injectMsg']
- [<moose.vec: class=PulseGen, id=729,path=/model/pulse>]
-
-Notice that the list contains something called vec. We discuss this
-`later <#some-more-details>`__. Also ``neighbors`` is a new kind of
-field: ``lookupFinfo`` which behaves like a dictionary. Next we connect
-the table to the soma to retrieve its membrane potential ``Vm``. This is
-where all those ``destFinfo`` starting with ``get`` or ``set`` come in
-use. For each value field ``X``, there is a ``destFinfo`` ``get{X}`` to
-retrieve the value at simulation time. This is used by the table to
-record the values ``Vm`` takes. ::
-
- >>> moose.connect(vmtab, 'requestOut', soma, 'getVm')
- <moose.SingleMsg: id=5, dataIndex=0, path=/Msgs[0]/singleMsg[0]>
-
-This finishes our model and recording setup. You might be wondering
-about the source-destination relationship above. It is natural to think
-that ``soma`` is the source of ``Vm`` values which should be sent to
-``vmtab``. But here ``requestOut`` is a ``srcFinfo`` acting like a
-reply card. This mode of obtaining data is called *pull* mode. [3]_
-
-You can skip the next section on fine control of the timing of updates
-and read :ref:`quickstart-running`.
-
-.. _quickstart-scheduling:
-
-Scheduling
-==========
-
-With the model all set up, we have to schedule the
-simulation. Different components in a model may have different rates
-of update. For example, the dynamics of electrical components require
-the update intervals to be of the order 0.01 ms whereas chemical
-components can be as slow as 1 s. Also, the results may depend on the
-sequence of the updates of different components. These issues are
-addressed in MOOSE using a clock-based update scheme. Each model
-component is scheduled on a clock tick (think of multiple hands of a
-clock ticking at different intervals and the object being updated at
-each tick of the corresponding hand). The scheduling also guarantees
-the correct sequencing of operations. For example, your Table objects
-should always be scheduled *after* the computations that they are
-recording, otherwise they will miss the outcome of the latest calculation.
-
-MOOSE has a central clock element (``/clock``) to manage
-time. Clock has a set of ``Tick`` elements under it that take care of
-advancing the state of each element with time as the simulation
-progresses. Every element to be included in a simulation must be
-assigned a tick. Each tick can have a different ticking interval
-(``dt``) that allows different elements to be updated at different
-rates.
-
-By default, every object is assigned a clock tick with reasonable default
-timesteps as soon it is created::
-
- Class type tick dt
- Electrical computations: 0-7 50 microseconds
- electrical compartments,
- V and ligand-gated ion channels,
- Calcium conc and Nernst,
- stimulus generators and tables,
- HSolve.
-
- Table (to plot elec. signals) 8 100 microseconds
-
- Diffusion solver 10 0.01 seconds
- Chemical computations: 11-17 0.1 seconds
- Pool, Reac, Enz, MMEnz,
- Func, Function,
- Gsolve, Ksolve,
- Stats (to do stats on outputs)
-
- Table2 (to plot chem. signals) 18 1 second
-
- HDF5DataWriter 30 1 second
- Postmaster (for parallel 31 0.01 seconds
- computations)
-
-There are 32 available clock ticks. Numbers 20 to 29 are
-unassigned so you can use them for whatever purpose you like.
-
-If you want fine control over the scheduling, there are three things
-you can do.
-
- * Alter the 'tick' field on the object
- * Alter the dt associated with a given tick, using the
- **moose.setClock( tick, newdt)** command
- * Go through a wildcard path of objects reassigning there clock ticks,
- using **moose.useClock( path, newtick, function)**.
-
-Here we discuss these in more detail.
-
-**Altering the 'tick' field**
-
-Every object knows which tick and dt it uses::
-
- >>> a = moose.Pool( '/a' )
- >>> print a.tick, a.dt
- 13 0.1
-
-The ``tick`` field on every object can be changed, and the object will
-adopt whatever clock dt is used for that tick. The ``dt`` field is
-readonly, because changing it would have side-effects on every object
-associated with the current tick.
-
-Ticks **-1** and **-2** are special: They both tell the object that it is
-disabled (not scheduled for any operations). An object with a
-tick of **-1** will be left alone entirely. A tick of **-2** is used in
-solvers to indicate that should the solver be removed, the object will
-revert to its default tick.
-
-**Altering the dt associated with a given tick**
-
-We initialize the ticks and set their ``dt`` values using the
-``setClock`` function. ::
-
- >>> moose.setClock(0, 0.025e-3)
- >>> moose.setClock(1, 0.025e-3)
- >>> moose.setClock(2, 0.25e-3)
-
-This will initialize tick #0 and tick #1 with ``dt = 25`` μs and tick #2
-with ``dt = 250`` μs. Thus all the elements scheduled on ticks #0 and 1
-will be updated every 25 μs and those on tick #2 every 250 μs. We use
-the faster clocks for the model components where finer timescale is
-required for numerical accuracy and the slower clock to sample the
-values of ``Vm``.
-
-Note that if you alter the dt associated with a given tick, this will
-affect the update time for *all* the objects using that clock tick. If
-you're unsure that you want to do this, use one of the vacant ticks.
-
-
-**Assigning clock ticks to all objects in a wildcard path**
-
-To assign tick #2 to the table for recording ``Vm``, we pass its
-whole path to the ``useClock`` function. ::
-
- >>> moose.useClock(2, '/data/soma_Vm', 'process')
-
-Read this as "use tick # 2 on the element at path ``/data/soma_Vm`` to
-call its ``process`` method at every step". Every class that is supposed
-to update its state or take some action during simulation implements a
-``process`` method. And in most cases that is the method we want the
-ticks to call at every time step. A less common method is ``init``,
-which is implemented in some classes to interleave actions or updates
-that must be executed in a specific order [4]_. The ``Compartment``
-class is one such case where a neuronal compartment has to know the
-``Vm`` of its neighboring compartments before it can calculate its
-``Vm`` for the next step. This is done with: ::
-
- >>> moose.useClock(0, soma.path, 'init')
-
-Here we used the ``path`` field instead of writing the path explicitly.
-
-Next we assign tick #1 to process method of everything under ``/model``. ::
-
- >>> moose.useClock(1, '/model/##', 'process')
-
-Here the second argument is an example of wild-card path. The ``##``
-matches everything under the path preceding it at any depth. Thus if we
-had some other objects under ``/model/soma``, ``process`` method of
-those would also have been scheduled on tick #1. This is very useful for
-complex models where it is tedious to scheduled each element
-individually. In this case we could have used ``/model/#`` as well for
-the path. This is a single level wild-card which matches only the
-children of ``/model`` but does not go farther down in the hierarchy.
-
-.. _quickstart-running:
-
-Running the simulation
-======================
-
-Once the model is all set up, we can put the model to its
-initial state using ::
-
- >>> moose.reinit()
-
-You may remember that we had changed initVm from ``-0.06`` to ``-0.07``.
-The reinit call we initialize ``Vm`` to that value. You can verify that ::
-
- >>> print soma.Vm
- -0.07
-
-Finally, we run the simulation for 300 ms ::
-
- >>> moose.start(300e-3)
-
-The data will be recorded by the ``soma_vm`` table, which is referenced
-by the variable ``vmtab``. The ``Table`` class provides a numpy array
-interface to its content. The field is ``vector``. So you can easily plot
-the membrane potential using the `matplotlib <http://matplotlib.org/>`__
-library. ::
-
- >>> import pylab
- >>> t = pylab.linspace(0, 300e-3, len(vmtab.vector))
- >>> pylab.plot(t, vmtab.vector)
- >>> pylab.show()
-
-The first line imports the pylab submodule from matplotlib. This useful
-for interactive plotting. The second line creates the time points to
-match our simulation time and length of the recorded data. The third
-line plots the ``Vm`` and the fourth line makes it visible. Does the
-plot match your expectation?
-
-.. _quickstart-details:
-
-Some more details
-=================
-
-``vec``, ``melement`` and ``element``
------------------------------------------
-
-MOOSE elements are instances of the class ``melement``. ``Compartment``,
-``PulseGen`` and other MOOSE classes are derived classes of
-``melement``. All ``melement`` instances are contained in array-like
-structures called ``vec``. Each ``vec`` object has a numerical
-``id_`` field uniquely identifying it. An ``vec`` can have one or
-more elements. You can create an array of elements ::
-
- >>> comp_array = moose.vec('/model/comp', n=3, dtype='Compartment')
-
-This tells MOOSE to create an ``vec`` of 3 ``Compartment`` elements
-with path ``/model/comp``. For ``vec`` objects with multiple
-elements, the index in the ``vec`` is part of the element path. ::
-
- >>> print comp_array.path, type(comp_array)
-
-shows that ``comp_array`` is an instance of ``vec`` class. You can
-loop through the elements in an ``vec`` like a Python list ::
-
- >>> for comp in comp_array:
- ... print comp.path, type(comp)
- ...
-
-shows ::
-
- /model/comp[0] <type 'moose.melement'>
- /model/comp[1] <type 'moose.melement'>
- /model/comp[2] <type 'moose.melement'>
-
-Thus elements are instances of class ``melement``. All elements in an
-``vec`` share the ``id_`` of the ``vec`` which can retrieved by
-``melement.getId()``.
-
-A frequent use case is that after loading a model from a file one knows
-the paths of various model components but does not know the appropriate
-class name for them. For this scenario there is a function called
-``element`` which converts ("casts" in programming jargon) a path or any
-moose object to its proper MOOSE class. You can create additional
-references to ``soma`` in the example this way ::
-
- x = moose.element('/model/soma')
-
-Any MOOSE class can be extended in Python. But any additional attributes
-added in Python are invisible to MOOSE. So those can be used for
-functionalities at the Python level only. You can see
-``moose-examples/squid/squid.py`` for an example.
-
-``Finfos``
-----------
-
-The following kinds of ``Finfo`` are accessible in Python
-
-- **``valueFinfo``** : simple values. For each readable ``valueFinfo``
- ``XYZ`` there is a ``destFinfo`` ``getXYZ`` that can be used for
- reading the value at run time. If ``XYZ`` is writable then there will
- also be ``destFinfo`` to set it: ``setXYZ``. Example:
- ``Compartment.Rm``
-- **``lookupFinfo``** : lookup tables. These fields act like Python
- dictionaries but iteration is not supported. Example:
- ``Neutral.neighbors``.
-- **``srcFinfo``** : source of a message. Example:
- ``PulseGen.output``.
-- **``destFinfo``** : destination of a message. Example:
- ``Compartment.injectMsg``. Apart from being used in setting up
- messages, these are accessible as functions from Python.
- ``HHGate.setupAlpha`` is an example.
-- **``sharedFinfo``** : a composition of source and destination fields.
- Example: ``Compartment.channel``.
-
-.. _quickstart-moving-on:
-
-Moving on
-=========
-
-Now you know the basics of pymoose and how to access the help
-system. You can figure out how to do specific things by looking at the
-:doc:`moose_cookbook`. In addition, the ``moose-examples/snippets`` directory
-in your MOOSE installation has small executable python scripts that
-show usage of specific classes or functionalities. Beyond that you can
-browse the code in the ``moose-examples`` directory to see some more complex
-models.
-
-MOOSE is backward compatible with GENESIS and most GENESIS classes have
-been reimplemented in MOOSE. There is slight change in naming (MOOSE
-uses CamelCase), and setting up messages are different. But `GENESIS
-documentation <http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual.html>`__
-is still a good source for documentation on classes that have been
-ported from GENESIS.
-
-If the built-in MOOSE classes do not satisfy your needs entirely, you
-are welcome to add new classes to MOOSE. The API documentation will
-help you get started. Finally, you can join the `moose mailing list
-<https://lists.sourceforge.net/lists/listinfo/moose-generic>`__ and
-request for help.
-
-
-.. [1]
- To list the classes only, use ``moose.le('/classes')``
-
-.. [2]
- MOOSE is unit agnostic and things should work fine as long as you use
- values all converted to a consistent unit system.
-
-.. [3]
- This apparently convoluted implementation is for performance reason.
- Can you figure out why? *Hint: the table is driven by a slower clock
- than the compartment.*
-
-.. [4]
- In principle any function available in a MOOSE class can be executed
- periodically this way as long as that class exposes the function for
- scheduling following the MOOSE API. So you have to consult the class'
- documentation for any nonstandard methods that can be scheduled this
- way.
diff --git a/moose-core/Docs/user/snippets_tutorial/Building_Simple_Reaction_Model.html b/moose-core/Docs/user/snippets_tutorial/Building_Simple_Reaction_Model.html
deleted file mode 100644
index 9523a502e38a436420e91b2332e724ee6cee2786..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/snippets_tutorial/Building_Simple_Reaction_Model.html
+++ /dev/null
@@ -1,588 +0,0 @@
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-<h2 id="This-example-illustrates-how-to-define-a-kinetic-model-using-the-scripting-interface.Normally-one-uses-standard-model-formats-like-SBML-or-kkit-to-concisely-define-kinetic-models,-but-in-some-cases-one-would-like-to-modify-the-model-through-the-script.">This example illustrates how to define a kinetic model using the scripting interface.Normally one uses standard model formats like SBML or kkit to concisely define kinetic models, but in some cases one would like to modify the model through the script.<a class="anchor-link" href="#This-example-illustrates-how-to-define-a-kinetic-model-using-the-scripting-interface.Normally-one-uses-standard-model-formats-like-SBML-or-kkit-to-concisely-define-kinetic-models,-but-in-some-cases-one-would-like-to-modify-the-model-through-the-script.">¶</a></h2><h2 id="This-example-creates-a-reaction-model">This example creates a reaction model<a class="anchor-link" href="#This-example-creates-a-reaction-model">¶</a></h2>
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-<div class=" highlight hl-ipython2"><pre><span class="c"># first step is to import moose</span>
-<span class="kn">import</span> <span class="nn">moose</span>
-<span class="kn">import</span> <span class="nn">pylab</span>
-<span class="kn">import</span> <span class="nn">numpy</span>
-<span class="o">%</span><span class="k">matplotlib</span> inline
-<span class="c"># create container for model</span>
-<span class="n">model</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Neutral</span><span class="p">(</span> <span class="s">'model'</span> <span class="p">)</span>
-
-<span class="c">#create chemical compartment either `CubeMesh` or `CylMesh` and set the volume</span>
-<span class="n">compartment</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">CubeMesh</span><span class="p">(</span> <span class="s">'/model/compartment'</span> <span class="p">)</span>
-<span class="n">compartment</span><span class="o">.</span><span class="n">volume</span> <span class="o">=</span> <span class="mf">1e-20</span>
-
-<span class="c"># create molecules and reactions</span>
-<span class="n">sub</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Pool</span><span class="p">(</span> <span class="s">'/model/compartment/Sub'</span> <span class="p">)</span>
-<span class="n">sub</span><span class="o">.</span><span class="n">concInit</span> <span class="o">=</span> <span class="mf">0.001</span>
-<span class="n">prd</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Pool</span><span class="p">(</span> <span class="s">'/model/compartment/Prd'</span> <span class="p">)</span>
-<span class="n">reac</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Reac</span><span class="p">(</span> <span class="s">'/model/compartment/reac'</span> <span class="p">)</span>
-<span class="n">reac</span><span class="o">.</span><span class="n">Kf</span> <span class="o">=</span> <span class="mf">0.1</span>
-<span class="n">reac</span><span class="o">.</span><span class="n">Kb</span> <span class="o">=</span> <span class="mf">0.001</span>
-
-<span class="c"># connect them up for reactions</span>
-<span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">reac</span><span class="p">,</span> <span class="s">'sub'</span><span class="p">,</span> <span class="n">sub</span><span class="p">,</span> <span class="s">'reac'</span> <span class="p">)</span>
-<span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">reac</span><span class="p">,</span> <span class="s">'prd'</span><span class="p">,</span> <span class="n">prd</span><span class="p">,</span> <span class="s">'reac'</span> <span class="p">)</span>
-
-
-<span class="c">#setting up the KSolve</span>
-<span class="n">gsolve</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Ksolve</span><span class="p">(</span> <span class="s">'/model/compartment/ksolve'</span> <span class="p">)</span>
-<span class="n">stoich</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Stoich</span><span class="p">(</span> <span class="s">'/model/compartment/stoich'</span> <span class="p">)</span>
-<span class="n">stoich</span><span class="o">.</span><span class="n">compartment</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment'</span> <span class="p">)</span>
-<span class="n">stoich</span><span class="o">.</span><span class="n">ksolve</span> <span class="o">=</span> <span class="n">gsolve</span>
-<span class="n">stoich</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="s">"/model/compartment/##"</span>
-<span class="n">moose</span><span class="o">.</span><span class="n">setClock</span><span class="p">(</span> <span class="mi">15</span><span class="p">,</span> <span class="mf">1.0</span> <span class="p">)</span> <span class="c"># clock for the solver</span>
-<span class="n">moose</span><span class="o">.</span><span class="n">useClock</span><span class="p">(</span> <span class="mi">15</span><span class="p">,</span> <span class="s">'/model/compartment/gsolve'</span><span class="p">,</span> <span class="s">'process'</span> <span class="p">)</span>
-
-<span class="c"># Create the output tables</span>
-<span class="n">graphs</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Neutral</span><span class="p">(</span> <span class="s">'/model/graphs'</span> <span class="p">)</span>
-<span class="n">outputA</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Table2</span> <span class="p">(</span> <span class="s">'/model/graphs/concA'</span> <span class="p">)</span>
-<span class="n">outputB</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Table2</span> <span class="p">(</span> <span class="s">'/model/graphs/concB'</span> <span class="p">)</span>
-
-<span class="c"># connect up the tables for plot substrate and product concentration</span>
-<span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">outputA</span><span class="p">,</span> <span class="s">'requestOut'</span><span class="p">,</span> <span class="n">sub</span><span class="p">,</span> <span class="s">'getConc'</span> <span class="p">);</span>
-<span class="n">moose</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span> <span class="n">outputB</span><span class="p">,</span> <span class="s">'requestOut'</span><span class="p">,</span> <span class="n">prd</span><span class="p">,</span> <span class="s">'getConc'</span> <span class="p">);</span>
-
-<span class="c"># reinit and run for 100s</span>
-<span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span>
-<span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span><span class="mi">100</span><span class="p">)</span>
-
-<span class="c">#setting up displaying plots in matplotlib</span>
-<span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/model/graphs/#[TYPE=Table2]'</span> <span class="p">):</span>
- <span class="n">t</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="c">#sec</span>
- <span class="n">pylab</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span><span class="p">,</span><span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
-<span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span>
-<span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
-</pre></div>
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diff --git a/moose-core/Docs/user/snippets_tutorial/Makefile b/moose-core/Docs/user/snippets_tutorial/Makefile
deleted file mode 100644
index 182070907cae692fced766d21141b1ccbc52a887..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/snippets_tutorial/Makefile
+++ /dev/null
@@ -1,153 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-PAPER =
-BUILDDIR = _build
-
-# Internal variables.
-PAPEROPT_a4 = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
-help:
- @echo "Please use \`make <target>' where <target> is one of"
- @echo " html to make standalone HTML files"
- @echo " dirhtml to make HTML files named index.html in directories"
- @echo " singlehtml to make a single large HTML file"
- @echo " pickle to make pickle files"
- @echo " json to make JSON files"
- @echo " htmlhelp to make HTML files and a HTML help project"
- @echo " qthelp to make HTML files and a qthelp project"
- @echo " devhelp to make HTML files and a Devhelp project"
- @echo " epub to make an epub"
- @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
- @echo " latexpdf to make LaTeX files and run them through pdflatex"
- @echo " text to make text files"
- @echo " man to make manual pages"
- @echo " texinfo to make Texinfo files"
- @echo " info to make Texinfo files and run them through makeinfo"
- @echo " gettext to make PO message catalogs"
- @echo " changes to make an overview of all changed/added/deprecated items"
- @echo " linkcheck to check all external links for integrity"
- @echo " doctest to run all doctests embedded in the documentation (if enabled)"
-
-clean:
- -rm -rf $(BUILDDIR)/*
-
-html:
- $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
- $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
- $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
- @echo
- @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
- $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
- @echo
- @echo "Build finished; now you can process the pickle files."
-
-json:
- $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
- @echo
- @echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
- $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
- @echo
- @echo "Build finished; now you can run HTML Help Workshop with the" \
- ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
- $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
- @echo
- @echo "Build finished; now you can run "qcollectiongenerator" with the" \
- ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
- @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/MOOSE.qhcp"
- @echo "To view the help file:"
- @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/MOOSE.qhc"
-
-devhelp:
- $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
- @echo
- @echo "Build finished."
- @echo "To view the help file:"
- @echo "# mkdir -p $$HOME/.local/share/devhelp/MOOSE"
- @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/MOOSE"
- @echo "# devhelp"
-
-epub:
- $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
- @echo
- @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-latex:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo
- @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
- @echo "Run \`make' in that directory to run these through (pdf)latex" \
- "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo "Running LaTeX files through pdflatex..."
- $(MAKE) -C $(BUILDDIR)/latex all-pdf
- @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text:
- $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
- @echo
- @echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man:
- $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
- @echo
- @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo
- @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
- @echo "Run \`make' in that directory to run these through makeinfo" \
- "(use \`make info' here to do that automatically)."
-
-info:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo "Running Texinfo files through makeinfo..."
- make -C $(BUILDDIR)/texinfo info
- @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext:
- $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
- @echo
- @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes:
- $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
- @echo
- @echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck:
- $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
- @echo
- @echo "Link check complete; look for any errors in the above output " \
- "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest:
- $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
- @echo "Testing of doctests in the sources finished, look at the " \
- "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/moose-core/Docs/user/snippets_tutorial/SteadyState.html b/moose-core/Docs/user/snippets_tutorial/SteadyState.html
deleted file mode 100644
index 3ab1625e9da32e16f58e46ac31b2f998e4891c60..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/snippets_tutorial/SteadyState.html
+++ /dev/null
@@ -1,919 +0,0 @@
-<!DOCTYPE html>
-<html>
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-
-<meta charset="utf-8" />
-<title>SteadyState</title>
-
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-<h1 id="Finding-a-Steady-State-in-MOOSE">Finding a Steady State in MOOSE<a class="anchor-link" href="#Finding-a-Steady-State-in-MOOSE">¶</a></h1>
-</div>
-</div>
-</div>
-<div class="cell border-box-sizing code_cell rendered">
-<div class="input">
-<div class="prompt input_prompt">In [1]:</div>
-<div class="inner_cell">
- <div class="input_area">
-<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">math</span>
-<span class="kn">import</span> <span class="nn">pylab</span>
-<span class="kn">import</span> <span class="nn">numpy</span>
-<span class="kn">import</span> <span class="nn">moose</span>
-
-<span class="o">%</span><span class="k">matplotlib</span> inline
-
-<span class="k">def</span> <span class="nf">displayPlots</span><span class="p">():</span>
- <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">moose</span><span class="o">.</span><span class="n">wildcardFind</span><span class="p">(</span> <span class="s">'/model/graphs/#'</span> <span class="p">):</span>
- <span class="n">t</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">1</span> <span class="p">)</span> <span class="c">#sec</span>
- <span class="n">pylab</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span> <span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="o">.</span><span class="n">vector</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="p">)</span>
- <span class="n">pylab</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span>
- <span class="n">pylab</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
-
-<span class="k">def</span> <span class="nf">getState</span><span class="p">(</span> <span class="n">ksolve</span><span class="p">,</span> <span class="n">state</span> <span class="p">):</span>
- <span class="n">state</span><span class="o">.</span><span class="n">randomInit</span><span class="p">()</span>
- <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">0.1</span> <span class="p">)</span> <span class="c"># Run the model for 2 seconds.</span>
- <span class="n">state</span><span class="o">.</span><span class="n">settle</span><span class="p">()</span>
- <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">20.0</span> <span class="p">)</span> <span class="c"># Run model for 10 seconds, just for display</span>
-
-
-<span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
- <span class="c">#One can build own model or load pre-existing model</span>
- <span class="c">#Here we have taken pre-existing model which is in cspace format</span>
- <span class="n">moose</span><span class="o">.</span><span class="n">loadModel</span><span class="p">(</span> <span class="s">'../../../../moose-examples/genesis/M1719.cspace'</span><span class="p">,</span> <span class="s">'/model'</span><span class="p">,</span> <span class="s">'ee'</span> <span class="p">)</span>
- <span class="n">compartment</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'model/kinetics'</span> <span class="p">)</span>
- <span class="n">compartment</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">'compartment'</span>
- <span class="c">#setting up the solver</span>
- <span class="n">ksolve</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Ksolve</span><span class="p">(</span> <span class="s">'/model/compartment/ksolve'</span> <span class="p">)</span>
- <span class="n">stoich</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">Stoich</span><span class="p">(</span> <span class="s">'/model/compartment/stoich'</span> <span class="p">)</span>
- <span class="n">stoich</span><span class="o">.</span><span class="n">compartment</span> <span class="o">=</span> <span class="n">compartment</span>
- <span class="n">stoich</span><span class="o">.</span><span class="n">ksolve</span> <span class="o">=</span> <span class="n">ksolve</span>
- <span class="n">stoich</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="s">"/model/compartment/##"</span>
- <span class="c">#setting up state</span>
- <span class="n">state</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">SteadyState</span><span class="p">(</span> <span class="s">'/model/compartment/state'</span> <span class="p">)</span>
-
- <span class="n">moose</span><span class="o">.</span><span class="n">reinit</span><span class="p">()</span>
- <span class="n">state</span><span class="o">.</span><span class="n">stoich</span> <span class="o">=</span> <span class="n">stoich</span>
- <span class="n">state</span><span class="o">.</span><span class="n">convergenceCriterion</span> <span class="o">=</span> <span class="mf">1e-7</span>
-
- <span class="n">a</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/a'</span> <span class="p">)</span>
- <span class="n">b</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/b'</span> <span class="p">)</span>
- <span class="n">c</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/c'</span> <span class="p">)</span>
-
- <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">100</span> <span class="p">):</span>
- <span class="n">getState</span><span class="p">(</span> <span class="n">ksolve</span><span class="p">,</span> <span class="n">state</span> <span class="p">)</span>
-
- <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">100.0</span> <span class="p">)</span> <span class="c"># Run the model for 100 seconds.</span>
-
- <span class="n">b</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/b'</span> <span class="p">)</span>
- <span class="n">c</span> <span class="o">=</span> <span class="n">moose</span><span class="o">.</span><span class="n">element</span><span class="p">(</span> <span class="s">'/model/compartment/c'</span> <span class="p">)</span>
-
- <span class="c"># move most molecules over to b</span>
- <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">+</span> <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">*</span> <span class="mf">0.95</span>
- <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">*</span> <span class="mf">0.05</span>
- <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">100.0</span> <span class="p">)</span> <span class="c"># Run the model for 100 seconds.</span>
-
- <span class="c"># move most molecules back to a</span>
- <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">conc</span> <span class="o">+</span> <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">*</span> <span class="mf">0.95</span>
- <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">conc</span> <span class="o">*</span> <span class="mf">0.05</span>
- <span class="n">moose</span><span class="o">.</span><span class="n">start</span><span class="p">(</span> <span class="mf">100.0</span> <span class="p">)</span> <span class="c"># Run the model for 100 seconds.</span>
-
- <span class="c"># Iterate through all plots, dump their contents to data.plot.</span>
- <span class="n">displayPlots</span><span class="p">()</span>
-
- <span class="n">quit</span><span class="p">()</span>
-
-<span class="c"># Run the 'main' if this script is executed standalone.</span>
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
- <span class="n">main</span><span class="p">()</span>
-</pre></div>
-
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-"
->
-</div>
-
-</div>
-
-</div>
-</div>
-
-</div>
-<div class="cell border-box-sizing code_cell rendered">
-<div class="input">
-<div class="prompt input_prompt">In [ ]:</div>
-<div class="inner_cell">
- <div class="input_area">
-<div class=" highlight hl-ipython2"><pre>
-</pre></div>
-
-</div>
-</div>
-</div>
-
-</div>
- </div>
- </div>
-</body>
-</html>
diff --git a/moose-core/Docs/user/snippets_tutorial/_templates/layout.html b/moose-core/Docs/user/snippets_tutorial/_templates/layout.html
deleted file mode 100644
index 75df84926246f910c90895c58dcb9a5bce462bb4..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/snippets_tutorial/_templates/layout.html
+++ /dev/null
@@ -1,33 +0,0 @@
-{% extends "!layout.html" %}
-{% block rootrellink %}
- <li><a href="http://moose.ncbs.res.in/">MOOSE Homepage</a> »</li>
- {{ super() }}
-{% endblock %}
-{% block sidebartitle %}
-
- {% if logo and theme_logo_only %}
- <a href="http://moose.ncbs.res.in">
-
- {% else %}
- <a href="http://moose.ncbs.res.in/" class="icon icon-home"> {{ project }}
- {% endif %}
-
- {% if logo %}
- {# Not strictly valid HTML, but it's the only way to display/scale it properly, without weird scripting or heaps of work #}
- <img src="{{ pathto('_static/' + logo, 1) }}" class="logo" />
- {% endif %}
- </a>
- {% if theme_display_version %}
- {%- set nav_version = version %}
- {% if READTHEDOCS and current_version %}
- {%- set nav_version = current_version %}
- {% endif %}
- {% if nav_version %}
- <div class="version">
- {{ nav_version }}
- </div>
- {% endif %}
- {% endif %}
-
- {% include "searchbox.html" %}
-{% endblock %}
diff --git a/moose-core/Docs/user/snippets_tutorial/conf.py b/moose-core/Docs/user/snippets_tutorial/conf.py
deleted file mode 100644
index b2b36b187bef3aa98b9dd0a21e98f19ce5d15ad2..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/snippets_tutorial/conf.py
+++ /dev/null
@@ -1,250 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# MOOSE documentation build configuration file, created by
-# sphinx-quickstart on Tue Jul 1 19:05:47 2014.
-#
-# This file is execfile()d with the current directory set to its containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-import sys, os
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('../../moose/moose-core/python'))
-sys.path.append(os.path.abspath('../../../../moose-examples/snippets'))
-# -- General configuration -----------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be extensions
-# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc',
- 'sphinx.ext.mathjax',
- 'sphinx.ext.autosummary',
- 'sphinx.ext.viewcode',
- 'numpydoc']
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix of source filenames.
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8-sig'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'MOOSE'
-copyright = u'2016'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '3.2'
-# The full version, including alpha/beta/rc tags.
-release = '3.2'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#language = None
-
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns = ['_build']
-
-# The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = True
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-
-# -- Options for HTML output ---------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages. See the documentation for
-# a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
-#html_theme = 'better'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further. For a list of options available for each theme, see the
-# documentation.
-# html_theme_options = {'stickysidebar': 'true',
-# 'sidebarwidth': '300'}
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = [better_theme_path]
-
-# The name for this set of Sphinx documents. If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-html_logo = '../../images/moose_logo.png'
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-#html_domain_indices = True
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
-
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it. The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'MOOSEdoc'
-
-
-# -- Options for LaTeX output --------------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
- ('index', 'MOOSE.tex', u'MOOSE Documentation',
- u'Upinder Bhalla, Aviral Goel and Harsha Rani', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-latex_logo = '../images/moose_logo.png'
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-latex_show_pagerefs = True
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-latex_domain_indices = True
-
-
-# -- Options for manual page output --------------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
- ('index', 'moose', u'MOOSE Documentation',
- [u'Upinder Bhalla, Aviral Goel and Harsha Rani'], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output ------------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-# dir menu entry, description, category)
-texinfo_documents = [
- ('index', 'MOOSE', u'MOOSE Documentation',
- u'Upinder Bhalla, Aviral Goel and Harsha Rani', 'MOOSE', 'MOOSE is the Multiscale Object-Oriented Simulation Environment.',
- 'Science'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-#numpydoc option
-numpydoc_show_class_members = True
diff --git a/moose-core/Docs/user/snippets_tutorial/index.rst b/moose-core/Docs/user/snippets_tutorial/index.rst
deleted file mode 100644
index c10ea58985b2ee8b14af34a847fcca22dbd0af00..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/snippets_tutorial/index.rst
+++ /dev/null
@@ -1,16 +0,0 @@
-.. MOOSE documentation master file, created by
- sphinx-quickstart on Tue Feb 2 14:05:47 2016.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Snippets and Tutorials for MOOSE
-==================================
-Snippets and Tutorials for MOOSE
-
-.. toctree::
- :maxdepth: 2
- :numbered:
-
-
- snippet
- tutorial
diff --git a/moose-core/Docs/user/snippets_tutorial/snippet.rst b/moose-core/Docs/user/snippets_tutorial/snippet.rst
deleted file mode 100644
index fff4d674d06b85384ed81dada2a03a1b7a804fb9..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/snippets_tutorial/snippet.rst
+++ /dev/null
@@ -1,66 +0,0 @@
-.. A snippets for MOOSE
-.. Lists all the snippets in moose-examples/snippets directory
-
-MOOSE Snippet
-==============
-
-The MOOSE Snippet contains examples showing you how to do specific
-tasks in MOOSE.
-
-Scripting Parser
-----------------
-
-Class features
---------------
-
-Network Models
---------------
-
-Single Neuron Models
----------------------
-Some salient properties of neuronal building blocks in MOOSE are described below.
-
-Signaling Pathways
-------------------
-This section show some of the chemical signaling pathways related settings
-
-Define a kinetic model using the scripting in moose
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: scriptKineticModel
- :members:
-
-Set up of kinetic solver
-^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: scriptKineticSolver
- :members:
-
-Multi scale models
--------------------
-
-3-D graphics
--------------
-
-Load-Run-Saving pre-existing model files
-----------------------------------------
-This section of the documentation explains how to load-run-save predefined models in MOOSE.
-
-Load Kinetics Models
-^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: loadKineticModel
- :members:
-
-Load SBML Models
-^^^^^^^^^^^^^^^^^
-.. automodule:: loadSbmlmodel
- :members:
-
-Load Cspace Models
-^^^^^^^^^^^^^^^^^^^
-.. automodule:: loadCspaceModel
- :members:
-
-Save Models to Sbml format
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. automodule:: convert_Genesis2Sbml
- :members:
-
diff --git a/moose-core/Docs/user/snippets_tutorial/tutorial.rst b/moose-core/Docs/user/snippets_tutorial/tutorial.rst
deleted file mode 100644
index 27a249832b91b4309a19983a280a3d94048e2c2d..0000000000000000000000000000000000000000
--- a/moose-core/Docs/user/snippets_tutorial/tutorial.rst
+++ /dev/null
@@ -1,37 +0,0 @@
-.. A tutorials for MOOSE
-.. This tutorials walks through some of the simple and practical approch related to MOOSE
-
-Audience
-This reference has been prepared for the beginners to help them understand the basic to advanced concepts related to MOOSE.
-This tutorial walks through a range of topics, including integrate-and-fire networks, chemical bistables, and oscillators.
-Has stand-alone graphics and the Python scripts are meant to tinker with.
-
-MOOSE Tutorial
-==============
-
-This reference has prepared for the users to help them understand from the basic to complex modeling building in MOOSE
-
-Chemical Signalling Models
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-`Load Kinetic Model <loadKineticModel.html>`_
-----------------------------------------------
-
-`Deterministic Simulation <DeterministicSolver.html>`_
-----------------------------------------------------------------
-
-`Stochastic Simulation <StochasticSolver.html>`_
------------------------------------------------------------
-
-`Finding Steady State <SteadyState.html>`_
--------------------------------------------------
-
-`Building Simple Reaction Model <Building_Simple_Reaction_Model.html>`_
-------------------------------------------------------------------------------
-
-
-
-Building of Electical Signalling Models
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Building Chemical-Electrical Signalling Models using Rdesigneur
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
diff --git a/moose-core/INSTALL.md b/moose-core/INSTALL.md
index e0ec061ae55f4e87b4764cc9b5ce974d2853065e..581e1a8708cc18caf066b2dfb7649a4975152fb6 100644
--- a/moose-core/INSTALL.md
+++ b/moose-core/INSTALL.md
@@ -135,7 +135,3 @@ and add this to your .bashrc file (if you use bash shell):
For other shells, look up your shell's manual to find out how to set environment
variable in it.
-
-# GUI
-
-Follow instructions given at https://github.com/BhallaLab/moose-gui
diff --git a/moose-core/Makefile b/moose-core/Makefile
index 3ed0b08aa859cad18e6a9c2cb674642803160a76..824a42986d8a0bfdf89679044e703b6a2ef22312 100644
--- a/moose-core/Makefile
+++ b/moose-core/Makefile
@@ -222,9 +222,9 @@ endif
# To use GSL, pass USE_GSL=true ( anything on the right will do) in make command line
ifdef USE_GSL
-#LIBS+= $(shell gsl-config --libs)
+LIBS+= $(shell gsl-config --libs)
#LIBS+= -L/usr/lib -Wl,--no-as-needed -lgsl -lgslcblas -lm
-LIBS+= -L/usr/lib -lgsl -lgslcblas -lm
+#LIBS+= -L/usr/lib -lgsl -lgslcblas -lm
CXXFLAGS+= -DUSE_GSL
else
LIBS+= -lm
diff --git a/moose-core/README.md b/moose-core/README.md
index e367419ec208171cf0ac06791f2e59f1f6a24408..b57d39f7a8a69b43df9501d0c2ec09b721632d1a 100644
--- a/moose-core/README.md
+++ b/moose-core/README.md
@@ -1,142 +1,8 @@
-[](https://travis-ci.org/BhallaLab/moose-core) [](https://readthedocs.org/projects/moose-core/?badge=latest)
-
-# MOOSE
-
-MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed
-to simulate neural systems ranging from subcellular components and biochemical
-reactions to complex models of single neurons, circuits, and large networks.
-MOOSE can operate at many levels of detail, from stochastic chemical
-computations, to multicompartment single-neuron models, to spiking neuron
-network models.
-
-MOOSE is multiscale: It can do all these calculations together. For example it
-handles interactions seamlessly between electrical and chemical signaling.
-MOOSE is object-oriented. Biological concepts are mapped into classes, and a
-model is built by creating instances of these classes and connecting them by
-messages. MOOSE also has classes whose job is to take over difficult
-computations in a certain domain, and do them fast. There are such solver
-classes for stochastic and deterministic chemistry, for diffusion, and for
-multicompartment neuronal models. MOOSE is a simulation environment, not just a
-numerical engine: It provides data representations and solvers (of course!), but
-also a scripting interface with Python, graphical displays with Matplotlib,
-PyQt, and OpenGL, and support for many model formats. These include SBML,
-NeuroML, GENESIS kkit and cell.p formats, HDF5 and NSDF for data writing.
-
-# VERSION
-
-This is MOOSE 3.0.2pre "Ghevar"
-
-# ABOUT VERSION 3.0.2, Ghevar
-
-The Ghevar release is the third of series 3 of MOOSE releases.
-
-Ghevar is a Rajasthani sweet with a stiff porous body soaked in sugar syrup.
-
-MOOSE 3.0.2pre is an evolutionary increment over 3.0.1::
-
-- There has been substantial development on the multiscale modeling front, with
-the implementation of the rdesigneur class and affiliated features.
-- MOOSE can now read NeuroMorpho .swc files natively.
-
-# LICENSE
-
-MOOSE is released under the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or (at
-your option) any later version.
-
-# HOMEPAGE
-
-http://moose.ncbs.res.in/
-
-
-# SOURCE REPOSITORY
-
-Old [SourceForge repository](https://sourceforge.net/projects/moose/) is no longer maintained. Current source repository is hosted on [github](https://github.com/BhallaLab/moose-core) with almost all revision history.
-
-
-# REQUIREMENTS
-
-## Core MOOSE
-
-- g++ (>= 4.4.x) REQUIRED For building the C++ MOOSE core.
-- GSL (>=1.16.x) or Boost (>=1.40) REQUIRED For core moose numerical computation
-- OpenMPI (1.8.x) OPTIONAL For running moose in parallel on clusters
-- SBML (5.9.x) OPTIONAL For reading and writing signalling models in SBML format
-- HDF5 (1.8.x) OPTIONAL For reading and writing data in HDF5 based formats
-
-## PyMOOSE REQUIRED except on cluster worker nodes
-
-Python interface for core MOOSE API
-
-In addition to core MOOSE requirements:
-
-- Python2 ( >= 2.6.x) or Python3 REQUIRED For building the MOOSE Python bindings
-- Python-dev ( >= 2.6.x) or python3-dev REQUIRED Python development headers and libraries
-- NumPy ( >= 1.6.x) REQUIRED For array interface
-
-## Graphical User Interface
-
-- PyQt4 (4.8.x) REQUIRED For Python GUI
-- Matplotlib ( >= 1.1.x) REQUIRED For plotting simulation results
-
-### Compartmental Model Visualization OPTIONAL
-
-- OSG (3.2.x) REQUIRED For 3D rendering and simulation of neuronal models
-- Qt4 (4.8.x) REQUIRED For C++ GUI of Moogli
-
-## Demos
-
-- PyQt4 (4.8.x) OPTIONAL GUI in squid demo, Traub et al 2005 demo.
-- NetworkX (1.x) OPTIONAL display neuronal topology in Traub et al 2005 demo.
-- Pygraphviz (1.x) OPTIONAL display neuronal topology in Traub et al 2005 demo.
-
-# AUTHORS
-
-- Upinder S. Bhalla - Primary Architect, Chemical kinetic solvers
-- Niraj Dudani - Neuronal solver
-- Subhasis Ray - PyMOOSE Design and Documentation, Python Plugin Interface, NSDF Format
-- G.V.HarshaRani - Web page design, SBML support, Kinetikit Plugin Development
-- Aditya Gilra - NeuroML reader development, integrate-and-fire neurons/networks, STDP
-- Aviral Goel - Moogli/Neurokit Development
-- Dilawar Singh - Packaging
-
-
-# Examples, tutorials and Demos:
-
-Look in the [moose-examples repository](https://github.com/BhallaLab/moose-examples) for sample code.
-
-- [tutorials](https://github.com/BhallaLab/moose-examples/tree/master/tutorials): Standalone scripts meant for teaching. Students are expected
- to modify the scripts to learn the principles of the models.
-- [squid](https://github.com/BhallaLab/moose-examples/tree/master/squid): The Hodkin-Huxley squid model, fully graphical interface.
-- [Genesis_files](https://github.com/BhallaLab/moose-examples/tree/master/Genesis_files): A number of kinetics models used in MOOSE demos.
-- [neuroml](https://github.com/BhallaLab/moose-examples/tree/master/neuroml): A number of NeuroML models used in MOOSE demos
-- [traub_2005](https://github.com/BhallaLab/moose-examples/tree/master/traub_2005): Example scripts for each of the individual cell models from
- the Traub 2005 thalamocortical model.
-- [snippets](https://github.com/BhallaLab/moose-examples/tree/master/snippets): Code snippets that can be used as building blocks and to
- illustrate how to use certain kinds of objects in MOOSE. These snippets are
- all meant to run as individual files.
-
-
-# Supported file formats.
-
-MOOSE comes with a NeuroML reader. Demos/neuroml has some python scripts showing
-how to load NeuroML models.
-
-MOOSE is backward compatible with GENESIS kinetikit. Demos/Genesis_files has
-some examples. You can load a kinetikit model with the loadModel function:
-
- moose.loadModel(kkit_file_path, modelname )
-
-MOOSE is backward compatible with GENESIS <model>.p files used for neuronal
-model specification. The same loadModel function can be used for this but you
-need to have all the channels used in the .p file preloaded in /library:
-
- moose.loadModel(prototype_file_path, modelname )
-
-MOOSE can also read .swc files from NeuroMorpho.org.
-
-# Documentation
-
-Complete MOOSE Documentation can be found at - http://moose.ncbs.res.in/content/view/5/6/
+[](https://travis-ci.org/BhallaLab/moose-core)
+This is core computational engine of [MOOSE simulator](https://github.com/BhallaLab/moose). This repository can be
+used to build the lasest python interface of MOOSE simulator. For more details
+see https://github.com/BhallaLab/moose/blob/master/README.md
+If you want to build `moose-python` using this repository, follow instructions given
+in https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md file.
diff --git a/moose-core/basecode/Makefile b/moose-core/basecode/Makefile
index bce67e6b969fd03d6e88ae4d62709fe66875149c..c4aa0eee61467e634ca9ee06ec5833d8b618654d 100644
--- a/moose-core/basecode/Makefile
+++ b/moose-core/basecode/Makefile
@@ -79,11 +79,11 @@ default: $(TARGET)
$(OBJ) : $(HEADERS) ../shell/Shell.h
Element.o: FuncOrder.h
-testAsync.o: SparseMatrix.h SetGet.h ../scheduling/Clock.h ../biophysics/IntFire.h ../synapse/SynHandlerBase.h ../synapse/SimpleSynHandler.h ../synapse/Synapse.h
+testAsync.o: SparseMatrix.h SetGet.h ../scheduling/Clock.h ../biophysics/IntFire.h ../synapse/SynHandlerBase.h ../synapse/SimpleSynHandler.h ../synapse/Synapse.h ../randnum/RNG.h
SparseMsg.o: SparseMatrix.h
SetGet.o: SetGet.h ../shell/Neutral.h
HopFunc.o: HopFunc.h ../mpi/PostMaster.h
-global.o: global.h
+global.o: global.h ../randnum/RNG.h
.cpp.o:
$(CXX) $(CXXFLAGS) -I../msg -I.. $< -c
diff --git a/moose-core/basecode/global.cpp b/moose-core/basecode/global.cpp
index 04434f083ff48c3eb16276c9ebff3567189058b4..c5c75f4633a3f6a5d3f18d6e25b07b7fe01c29aa 100644
--- a/moose-core/basecode/global.cpp
+++ b/moose-core/basecode/global.cpp
@@ -99,17 +99,17 @@ namespace moose {
return moose::rng.uniform( );
}
- // Fix the given path.
- string createPosixPath( const string& path )
+ // MOOSE suffixes [0] to all elements to path. Remove [0] with null
+ // character whenever possible. For n > 0, [n] should not be touched. Its
+ // the user job to take the pain and write the correct path.
+ string createMOOSEPath( const string& path )
{
string s = path; /* Local copy */
- string undesired = ":?\"<>|[]";
-
- for (size_t i = 0; i < s.size() ; ++i)
- {
- bool found = undesired.find(s[i]) != string::npos;
- if(found) s[i] = '_';
- }
+ // Remove [0] from paths. They will be annoying for normal users.
+ std::string::size_type n = 0;
+ string zeroIndex("[0]");
+ while( (n = s.find( zeroIndex, n )) != std::string::npos )
+ s.erase( n, zeroIndex.size() );
return s;
}
@@ -204,14 +204,9 @@ namespace moose {
/* /a[0]/b[1]/c[0] -> /a/b/c */
string moosePathToUserPath( string path )
{
- size_t p1 = path.find( '[', 0 );
- while( p1 != std::string::npos )
- {
- size_t p2 = path.find( ']', p1 );
- path.erase( p1, p2-p1+1 );
- p1 = path.find( '[', p2 );
- }
- return path;
+ // Just write the moose path. Things becomes messy when indexing is
+ // used.
+ return createMOOSEPath( path );
}
/* Return formatted string
diff --git a/moose-core/basecode/global.h b/moose-core/basecode/global.h
index 6994212db187e7ca649b8b3b47b7c237c73b36a3..9b06b2820245f1ef4d8fd0639be1b3e6f42a5a13 100644
--- a/moose-core/basecode/global.h
+++ b/moose-core/basecode/global.h
@@ -17,7 +17,6 @@
#include <sstream>
-
#ifdef USE_BOOST
//#ifdef BOOST_FILESYSTEM_EXISTS
#include <boost/filesystem.hpp>
@@ -126,7 +125,7 @@ namespace moose
* @param path Reutrn path is given path if creation was successful, else
* directory is renamed to a filename.
*/
- string createPosixPath( const string& path );
+ string createMOOSEPath( const string& path );
/**
* @brief Convert a given value to string.
diff --git a/moose-core/biophysics/MarkovChannel.cpp b/moose-core/biophysics/MarkovChannel.cpp
index dbb82eb357da96822efca362cf3bc3d068165654..47991d19e19d0a81632bc77000c5be7579e6b52d 100644
--- a/moose-core/biophysics/MarkovChannel.cpp
+++ b/moose-core/biophysics/MarkovChannel.cpp
@@ -14,7 +14,10 @@
#include "ChanBase.h"
#include "ChanCommon.h"
#include "MarkovChannel.h"
+
+#if USE_GSL
#include <gsl/gsl_errno.h>
+#endif
const Cinfo* MarkovChannel::initCinfo()
{
diff --git a/moose-core/builtins/Streamer.cpp b/moose-core/builtins/Streamer.cpp
index 836e3c2b5faf2c1bcf3ee248c3d35f142e3b0337..93d4419411ce35fea94b37a2911a8da8ca08fe17 100644
--- a/moose-core/builtins/Streamer.cpp
+++ b/moose-core/builtins/Streamer.cpp
@@ -21,6 +21,9 @@
#include "header.h"
#include "Streamer.h"
#include "Clock.h"
+#include "utility/utility.h"
+#include "../shell/Shell.h"
+
const Cinfo* Streamer::initCinfo()
{
@@ -141,7 +144,8 @@ Streamer::Streamer()
columns_.push_back( "time" ); /* First column is time. */
tables_.resize(0);
tableIds_.resize(0);
- columns_.resize(0);
+ tableTick_.resize(0);
+ tableDt_.resize(0);
data_.resize(0);
}
@@ -171,9 +175,67 @@ void Streamer::cleanUp( void )
*/
void Streamer::reinit(const Eref& e, ProcPtr p)
{
+
+ if( tables_.size() == 0 )
+ {
+ moose::showWarn( "Zero tables in streamer. Disabling Streamer" );
+ e.element()->setTick( -2 ); /* Disable process */
+ return;
+ }
+
+ Clock* clk = reinterpret_cast<Clock*>( Id(1).eref().data() );
+ for (size_t i = 0; i < tableIds_.size(); i++)
+ {
+ int tickNum = tableIds_[i].element()->getTick();
+ double tick = clk->getTickDt( tickNum );
+ tableDt_.push_back( tick );
+ // Make sure that all tables have the same tick.
+ if( i > 0 )
+ {
+ if( tick != tableDt_[0] )
+ {
+ moose::showWarn( "Table " + tableIds_[i].path() + " has "
+ " different clock dt. "
+ " Make sure all tables added to Streamer have the same "
+ " dt value."
+ );
+ }
+ }
+ }
+
+
// Push each table dt_ into vector of dt
for( size_t i = 0; i < tables_.size(); i++)
- tableDt_.push_back( tables_[i]->getDt() );
+ {
+ Id tId = tableIds_[i];
+ int tickNum = tId.element()->getTick();
+ tableDt_.push_back( clk->getTickDt( tickNum ) );
+ }
+
+
+ // Make sure all tables have same dt_ else disable the streamer.
+ vector<unsigned int> invalidTables;
+ for (size_t i = 1; i < tableTick_.size(); i++)
+ {
+ if( tableTick_[i] != tableTick_[0] )
+ {
+ LOG( moose::warning
+ , "Table " << tableIds_[i].path()
+ << " has tick (dt) which is different than the first table."
+ << endl
+ << " Got " << tableTick_[i] << " expected " << tableTick_[0]
+ << endl << " Disabling this table."
+ );
+ invalidTables.push_back( i );
+ }
+ }
+
+ for (size_t i = 0; i < invalidTables.size(); i++)
+ {
+ tables_.erase( tables_.begin() + i );
+ tableDt_.erase( tableDt_.begin() + i );
+ tableIds_.erase( tableIds_.begin() + i );
+ }
if( ! isOutfilePathSet_ )
{
@@ -198,10 +260,9 @@ void Streamer::process(const Eref& e, ProcPtr p)
// Prepare data.
zipWithTime( data_, currTime_ );
StreamerBase::writeToOutFile( outfilePath_, format_, "a", data_, columns_ );
+
// clean the arrays
data_.clear();
- for(size_t i = 0; i < tables_.size(); i++ )
- tables_[i]->clearVec();
}
@@ -218,13 +279,16 @@ void Streamer::addTable( Id table )
return; /* Already added. */
Table* t = reinterpret_cast<Table*>(table.eref().data());
-
tableIds_.push_back( table );
tables_.push_back( t );
+ tableTick_.push_back( table.element()->getTick() );
- // We don't want name of table here as column names since they may not be
- // unique. However, paths of tables are guarenteed to be unique.
- columns_.push_back( moose::moosePathToUserPath( table.path() ) );
+ // NOTE: If user can make sure that names are unique in table, using name is
+ // better than using the full path.
+ if( t->getName().size() > 0 )
+ columns_.push_back( t->getName( ) );
+ else
+ columns_.push_back( moose::moosePathToUserPath( table.path() ) );
}
/**
@@ -234,6 +298,8 @@ void Streamer::addTable( Id table )
*/
void Streamer::addTables( vector<Id> tables )
{
+ if( tables.size() == 0 )
+ return;
for( vector<Id>::const_iterator it = tables.begin(); it != tables.end(); it++)
addTable( *it );
}
@@ -326,4 +392,8 @@ void Streamer::zipWithTime( vector<double>& data, double currTime)
for( size_t i = 0; i < tables_.size(); i++)
data.push_back( tables_[i]->getVec()[i] );
}
+
+ // clear the data from tables now.
+ for(size_t i = 0; i < tables_.size(); i++ )
+ tables_[i]->clearVec();
}
diff --git a/moose-core/builtins/Streamer.h b/moose-core/builtins/Streamer.h
index b1d29f1833b06556666f37327f8d83ac37083a41..738788a9508b6aa2c04f0a901c2bbe994563c88c 100644
--- a/moose-core/builtins/Streamer.h
+++ b/moose-core/builtins/Streamer.h
@@ -76,8 +76,9 @@ private:
string format_;
bool isOutfilePathSet_;
- // dt_ of Table's clock
+ // dt_ and tick number of Table's clock
vector<double> tableDt_;
+ vector<unsigned int> tableTick_;
// This currTime is not computed using the ProcPtr but rather using Tables
// dt_ and number of entries written.
diff --git a/moose-core/builtins/StreamerBase.cpp b/moose-core/builtins/StreamerBase.cpp
index af5f08a2d8fc528dec4b04984c64c3b1f891ebf2..90904c34b751cd6148440e19a14de591f969961b 100644
--- a/moose-core/builtins/StreamerBase.cpp
+++ b/moose-core/builtins/StreamerBase.cpp
@@ -62,8 +62,6 @@ void StreamerBase::writeToOutFile( const string& filepath
, const vector<string>& columns
)
{
- //cout << "Format " << outputFormat << " size is " << data.size() << endl;
-
if( data.size() == 0 )
return;
@@ -100,7 +98,7 @@ void StreamerBase::writeToCSVFile( const string& filepath, const string& openmod
string headerText = "";
for( vector<string>::const_iterator it = columns.begin();
it != columns.end(); it++ )
- headerText += "\"" + *it + "\"" + delimiter_;
+ headerText += ( *it + delimiter_ );
headerText += eol;
fprintf( fp, "%s", headerText.c_str() );
}
@@ -123,7 +121,6 @@ void StreamerBase::writeToCSVFile( const string& filepath, const string& openmod
void StreamerBase::writeToNPYFile( const string& filepath, const string& openmode
, const vector<double>& data, const vector<string>& columns )
{
- string format = moose::getExtension( filepath, true );
cnpy2::save_numpy<double>( filepath, data, columns, openmode );
}
diff --git a/moose-core/builtins/Table.cpp b/moose-core/builtins/Table.cpp
index 8b3049204c48c3cd168de8b60d0485f5b95e12ac..c9c641809b826fd039fe286efd781b2b03066fdc 100644
--- a/moose-core/builtins/Table.cpp
+++ b/moose-core/builtins/Table.cpp
@@ -74,6 +74,13 @@ const Cinfo* Table::initCinfo()
, &Table::getFormat
);
+ static ValueFinfo< Table, string > name(
+ "name"
+ , "Name of the table."
+ , &Table::setName
+ , &Table::getName
+ );
+
//////////////////////////////////////////////////////////////
// MsgDest Definitions
//////////////////////////////////////////////////////////////
@@ -119,6 +126,7 @@ const Cinfo* Table::initCinfo()
{
&threshold, // Value
&format, // Value
+ &name, // Value
&outfile, // Value
&useStreamer, // Value
handleInput(), // DestFinfo
@@ -190,7 +198,7 @@ const Cinfo* Table::initCinfo()
static const Cinfo* tableCinfo = Table::initCinfo();
-Table::Table() : threshold_( 0.0 ) , lastTime_( 0.0 ) , input_( 0.0 )
+Table::Table() : threshold_( 0.0 ) , lastTime_( 0.0 ) , input_( 0.0 ), dt_( 0.0 )
{
// Initialize the directory to which each table should stream.
rootdir_ = "_tables";
@@ -339,6 +347,17 @@ string Table::getFormat( void ) const
return format_;
}
+/* User defined name */
+string Table::getName( void ) const
+{
+ return tableName_;
+}
+
+void Table::setName( const string name )
+{
+ tableName_ = name ;
+}
+
/* Enable/disable streamer support. */
void Table::setUseStreamer( bool useStreamer )
{
@@ -353,7 +372,7 @@ bool Table::getUseStreamer( void ) const
/* set/get outfile_ */
void Table::setOutfile( string outpath )
{
- outfile_ = moose::createPosixPath( outpath );
+ outfile_ = moose::createMOOSEPath( outpath );
if( ! moose::createParentDirs( outfile_ ) )
outfile_ = moose::toFilename( outfile_ );
diff --git a/moose-core/builtins/Table.h b/moose-core/builtins/Table.h
index fffc477cd9e93288d5a59071db1e7546882f09d4..3e2e086e3d4b6671f8308b9edd5d6ce158152574 100644
--- a/moose-core/builtins/Table.h
+++ b/moose-core/builtins/Table.h
@@ -34,9 +34,12 @@ public:
void setThreshold( double v );
double getThreshold() const;
- void setFormat( string format );
+ void setFormat( const string format );
string getFormat( ) const;
+ void setName( const string name );
+ string getName( ) const;
+
void setUseStreamer( bool status );
bool getUseStreamer( void ) const;
diff --git a/moose-core/builtins/testNSDF.cpp b/moose-core/builtins/testNSDF.cpp
index 89b11e6dbd43584e7b97e4fe6ffa1c6a6f4aefa2..18283748ad6370009c6f1ff100eda4d3cfcae37a 100644
--- a/moose-core/builtins/testNSDF.cpp
+++ b/moose-core/builtins/testNSDF.cpp
@@ -52,6 +52,7 @@
#include <ctime>
#include <deque>
+#include <cstdio>
#include "header.h"
#include "../utility/utility.h"
@@ -62,7 +63,6 @@
#include "NSDFWriter.h"
#include "InputVariable.h"
-#define FILENAME "/tmp/HDF_testCreateStringDataset.h5"
#define STR_DSET_NAME "vlenstr_dset"
#define STR_DSET_LEN 4
@@ -73,7 +73,8 @@ void testCreateStringDataset()
hsize_t size = STR_DSET_LEN;
herr_t status;
HDF5WriterBase writer;
- file = H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ string h5Filename = std::tmpnam( NULL );
+ file = H5Fcreate(h5Filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
dset = writer.createStringDataset(file, STR_DSET_NAME, size, size);
assert(dset >= 0);
memtype = H5Tcopy(H5T_C_S1);
diff --git a/moose-core/ksolve/GssaVoxelPools.cpp b/moose-core/ksolve/GssaVoxelPools.cpp
index 57af561d51544b9e6c609f9dbcb6c0dc4b708b53..c7eaba66b091641b15c831a52ddf617776b5393d 100644
--- a/moose-core/ksolve/GssaVoxelPools.cpp
+++ b/moose-core/ksolve/GssaVoxelPools.cpp
@@ -48,15 +48,13 @@ const double SAFETY_FACTOR = 1.0 + 1.0e-9;
//////////////////////////////////////////////////////////////
GssaVoxelPools::GssaVoxelPools() :
- VoxelPoolsBase(), t_( 0.0 ), atot_( 0.0 ), rng_( new moose::RNG<double>() )
-{
-}
+ VoxelPoolsBase(), t_( 0.0 ), atot_( 0.0 )
+{ ; }
GssaVoxelPools::~GssaVoxelPools()
{
for ( unsigned int i = 0; i < rates_.size(); ++i )
delete( rates_[i] );
- delete rng_;
}
//////////////////////////////////////////////////////////////
@@ -101,7 +99,7 @@ void GssaVoxelPools::updateDependentRates(
unsigned int GssaVoxelPools::pickReac()
{
- double r = rng_->uniform( ) * atot_;
+ double r = rng_.uniform( ) * atot_;
double sum = 0.0;
// This is an inefficient way to do it. Can easily get to
@@ -161,7 +159,9 @@ void GssaVoxelPools::recalcTime( const GssaSystem* g, double currTime )
refreshAtot( g );
assert( t_ > currTime );
t_ = currTime;
- double r = rng_->uniform(std::numeric_limits<double>::min(), 1.0);
+ double r = rng_.uniform( );
+ while( r == 0.0 )
+ r = rng_.uniform( );
t_ -= ( 1.0 / atot_ ) * log( r );
}
@@ -201,10 +201,10 @@ void GssaVoxelPools::advance( const ProcInfo* p, const GssaSystem* g )
double sign = double(v_[rindex] >= 0) - double(0 > v_[rindex] );
g->transposeN.fireReac( rindex, Svec(), sign );
- double r = rng_->uniform();
+ double r = rng_.uniform();
while ( r <= 0.0 )
{
- r = rng_->uniform();
+ r = rng_.uniform();
}
t_ -= ( 1.0 / atot_ ) * log( r );
// g->stoich->updateFuncs( varS(), t_ ); // Handled next line.
@@ -215,12 +215,13 @@ void GssaVoxelPools::advance( const ProcInfo* p, const GssaSystem* g )
void GssaVoxelPools::reinit( const GssaSystem* g )
{
- rng_->setSeed( moose::__rng_seed__ );
+ //rng_.setSeed( moose::__rng_seed__ );
VoxelPoolsBase::reinit(); // Assigns S = Sinit;
+ unsigned int numVarPools = g->stoich->getNumVarPools();
g->stoich->updateFuncs( varS(), 0 );
- unsigned int numVarPools = g->stoich->getNumVarPools();
double* n = varS();
+
if ( g->useRandInit )
{
// round up or down probabilistically depending on fractional
@@ -230,8 +231,7 @@ void GssaVoxelPools::reinit( const GssaSystem* g )
double base = floor( n[i] );
assert( base >= 0.0 );
double frac = n[i] - base;
- // if ( gsl_rng_->uniform( rng ) > frac )
- if ( rng_->uniform() > frac )
+ if ( rng_.uniform() > frac )
n[i] = base;
else
n[i] = base + 1.0;
@@ -340,7 +340,7 @@ void GssaVoxelPools::setVolumeAndDependencies( double vol )
static double integralTransfer( double propensity )
{
double t= floor( propensity );
- if ( rng_->uniform() < propensity - t )
+ if ( rng_.uniform() < propensity - t )
return t + 1;
return t;
}
@@ -362,7 +362,7 @@ void GssaVoxelPools::xferIn( XferInfo& xf,
// cout << x << " i = " << *i << *j << " m = " << *m << endl;
double dx = *i++ - *j++;
double base = floor( dx );
- if ( rng_->uniform() > dx - base )
+ if ( rng_.uniform() > dx - base )
x += base;
else
x += base + 1.0;
@@ -416,7 +416,7 @@ void GssaVoxelPools::xferInOnlyProxies(
if ( *k >= stoichPtr_->getNumVarPools() && *k < proxyEndIndex )
{
double base = floor( *i );
- if ( rng_->uniform() > *i - base )
+ if ( rng_.uniform() > *i - base )
varSinit()[*k] = (varS()[*k] += base );
else
varSinit()[*k] = (varS()[*k] += base + 1.0 );
diff --git a/moose-core/ksolve/GssaVoxelPools.h b/moose-core/ksolve/GssaVoxelPools.h
index 18b08aa0d79dfa7d65bc5a3ed0d4c6958e8c2a89..ec062b46e89ef723e6431188f8608b24019cfec3 100644
--- a/moose-core/ksolve/GssaVoxelPools.h
+++ b/moose-core/ksolve/GssaVoxelPools.h
@@ -100,7 +100,7 @@ private:
/**
* @brief RNG.
*/
- moose::RNG<double>* rng_;
+ moose::RNG<double> rng_;
};
diff --git a/moose-core/ksolve/Makefile b/moose-core/ksolve/Makefile
index 5ca1bbcacf87f55e0f29f732d4571da2a53c58fe..49b51df4a418ed42d20c7aa9c64bcd06d63c0806 100644
--- a/moose-core/ksolve/Makefile
+++ b/moose-core/ksolve/Makefile
@@ -65,9 +65,10 @@ KinSparseMatrix.o: KinSparseMatrix.h ../basecode/SparseMatrix.h
ZombiePool.o: ../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h ../kinetics/lookupVolumeFromMesh.h
ZombieBufPool.o: ../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h ZombieBufPool.h ../kinetics/lookupVolumeFromMesh.h
ZombieBufPool.o: ../kinetics/PoolBase.h ZombiePoolInterface.h ZombiePool.h
-VoxelPoolsBase.o: VoxelPoolsBase.h
+VoxelPoolsBase.o: VoxelPoolsBase.h ../randnum/RNG.h
VoxelPools.o: VoxelPoolsBase.h VoxelPools.h OdeSystem.h RateTerm.h Stoich.h
-GssaVoxelPools.o: VoxelPoolsBase.h GssaVoxelPools.h ../basecode/SparseMatrix.h KinSparseMatrix.h GssaSystem.h RateTerm.h Stoich.h
+GssaVoxelPools.o: VoxelPoolsBase.h GssaVoxelPools.h ../basecode/SparseMatrix.h \
+ ../randnum/RNG.h KinSparseMatrix.h GssaSystem.h RateTerm.h Stoich.h
RateTerm.o: RateTerm.h
FuncTerm.o: FuncTerm.h
Stoich.o: RateTerm.h FuncTerm.h FuncRateTerm.h Stoich.h ../kinetics/PoolBase.h ../kinetics/ReacBase.h ../kinetics/EnzBase.h ../kinetics/CplxEnzBase.h ../basecode/SparseMatrix.h KinSparseMatrix.h ../scheduling/Clock.h ZombiePoolInterface.h
diff --git a/moose-core/ksolve/NonLinearSystem.h b/moose-core/ksolve/NonLinearSystem.h
deleted file mode 100644
index 24c5c4ea7e13896ba7aab2aadcb3e5f5d69c31b8..0000000000000000000000000000000000000000
--- a/moose-core/ksolve/NonLinearSystem.h
+++ /dev/null
@@ -1,332 +0,0 @@
-/*
- * =====================================================================================
- *
- * Description: Compute root of a multi-dimensional system using boost
- * libraries.
- *
- * Version: 1.0
- * Created: 04/13/2016 11:31:37 AM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Dilawar Singh (), dilawars@ncbs.res.in
- * Organization: NCBS Bangalore
- *
- * =====================================================================================
- */
-
-#include <iostream>
-#include <sstream>
-#include <functional>
-#include <cerrno>
-#include <iomanip>
-#include <limits>
-#include <algorithm>
-
-// Boost ublas library of matrix algebra.
-#include <boost/numeric/ublas/matrix.hpp>
-#include <boost/numeric/ublas/lu.hpp>
-#include <boost/numeric/ublas/vector.hpp>
-#include <boost/numeric/ublas/io.hpp>
-
-
-#include "VoxelPools.h"
-
-using namespace std;
-using namespace boost::numeric;
-
-typedef double value_type;
-typedef ublas::vector<value_type> vector_type;
-typedef ublas::matrix<value_type> matrix_type;
-
-
-class ReacInfo
-{
-public:
- int rank;
- int num_reacs;
- size_t num_mols;
- int nIter;
- double convergenceCriterion;
- double* T;
- VoxelPools* pool;
- vector< double > nVec;
- ublas::matrix< value_type > Nr;
- ublas::matrix< value_type > gamma;
-};
-
-
-/* Matrix inversion routine.
- Uses lu_factorize and lu_substitute in uBLAS to invert a matrix */
-template<class T>
-bool inverse(const ublas::matrix<T>& input, ublas::matrix<T>& inverse)
-{
- using namespace boost::numeric::ublas;
- typedef permutation_matrix<std::size_t> pmatrix;
- // create a working copy of the input
- matrix<T> A(input);
- // create a permutation matrix for the LU-factorization
- pmatrix pm(A.size1());
-
- // perform LU-factorization
- int res = lu_factorize(A,pm);
- if( res != 0 ) return false;
-
- // create identity matrix of "inverse"
- inverse.assign(ublas::identity_matrix<T>(A.size1()));
-
- // backsubstitute to get the inverse
- lu_substitute(A, pm, inverse);
-
- return true;
-}
-
-// A sysmte of non-linear equations. Store the values in result.
-class NonlinearSystem
-{
-public:
-
- NonlinearSystem( size_t systemSize ) : size_( systemSize )
- {
- f_.resize( size_, 0);
- slopes_.resize( size_, 0);
- x_.resize( size_, 0 );
-
- J_.resize( size_, size_, 0);
- invJ_.resize( size_, size_, 0);
-
- x2.resize( size_, 0);
- x1.resize( size_, 0);
-
- ri.nVec.resize( size_ );
- dx_ = sqrt( numeric_limits<double>::epsilon() );
- }
-
- vector_type compute_at(const vector_type& x)
- {
- vector_type result( size_ );
- system(x, result);
- return result;
- }
-
- int apply( )
- {
- return system(x_, f_);
- }
-
- int compute_jacobians( const vector_type& x, bool compute_inverse = true )
- {
- for( size_t i = 0; i < size_; i++)
- for( size_t j = 0; j < size_; j++)
- {
- vector_type temp = x;
- temp[j] += dx_;
- J_(i, j) = (compute_at(temp)[i] - compute_at(x)[i]) / dx_;
- }
-
- // is_jacobian_valid_ = true;
- // Keep the inverted J_ ready
- //if(is_jacobian_valid_ and compute_inverse )
- if( compute_inverse )
- inverse( J_, invJ_ );
-
- return 0;
- }
-
- template<typename T>
- void initialize( const T& x )
- {
- vector_type init;
- init.resize(size_, 0);
-
- for( size_t i = 0; i < size_; i++)
- init[i] = x[i];
-
- x_ = init;
- apply();
-
- compute_jacobians( init );
- }
-
- string to_string( )
- {
- stringstream ss;
-
- ss << "=======================================================";
- ss << endl << setw(25) << "State of system: " ;
- ss << " Argument: " << x_ << " Value : " << f_;
- ss << endl << setw(25) << "Jacobian: " << J_;
- ss << endl << setw(25) << "Inverse Jacobian: " << invJ_;
- ss << endl;
- return ss.str();
- }
-
- int system( const vector_type& x, vector_type& f )
- {
- int num_consv = ri.num_mols - ri.rank;
- for ( size_t i = 0; i < ri.num_mols; ++i )
- {
- double temp = x[i] * x[i] ;
-
-#if 0
- // if overflow
- if ( std::isnan( temp ) or std::isinf( temp ) )
- {
- cerr << "Failed: ";
- for( auto v : ri.nVec ) cerr << v << ", ";
- cerr << endl;
- return -1;
- }
-#endif
- ri.nVec[i] = temp;
- }
-
- vector< double > vels;
- ri.pool->updateReacVelocities( &ri.nVec[0], vels );
-
- assert( vels.size() == static_cast< unsigned int >( ri.num_reacs ) );
-
- // y = Nr . v
- // Note that Nr is row-echelon: diagonal and above.
- for ( int i = 0; i < ri.rank; ++i )
- {
- double temp = 0;
- for ( int j = i; j < ri.num_reacs; ++j )
- temp += ri.Nr(i, j ) * vels[j];
- f[i] = temp ;
- }
-
- // dT = gamma.S - T
- for ( int i = 0; i < num_consv; ++i )
- {
- double dT = - ri.T[i];
- for ( size_t j = 0; j < ri.num_mols; ++j )
- dT += ri.gamma(i, j) * x[j] * x[j];
-
- f[ i + ri.rank] = dT ;
- }
- return 0;
- }
-
-
- /**
- * @brief Find roots using Newton-Raphson method.
- *
- * @param tolerance 1e-7
- * @param max_iter Maximum number of iteration allowed , default 100
- *
- * @return If successful, return true. Check the variable `x_` at
- * which the system f_ is close to zero (within the tolerance).
- */
- bool find_roots_gnewton( double tolerance = 1e-7 , size_t max_iter = 50)
- {
- //tolerance = sqrt( numeric_limits<double>::epsilon() );
- double norm2OfDiff = 1.0;
- size_t iter = 0;
- int status = apply();
-
- while( ublas::norm_2(f_) >= tolerance )
- {
- iter += 1;
- compute_jacobians( x_, true );
- vector_type correction = ublas::prod( invJ_, f_ );
- x_ -= correction;
-
- // If could not compute the value of system successfully.
- status = apply();
- if( 0 != status )
- return false;
-
- if( iter >= max_iter )
- break;
-
- }
-
- ri.nIter = iter;
-
- if( iter >= max_iter )
- return false;
-
- return true;
- }
-
- /**
- * @brief Compute the slope of function in given dimension.
- *
- * @param which_dimen The index of dimension.
- *
- * @return Slope.
- */
- value_type slope( unsigned int which_dimen )
- {
- vector_type x = x_;
- x[which_dimen] += dx_;
- // x1 and x2 holds the f_ of system at x_ and x (which is x +
- // some step)
- system( x_, x1 );
- system( x, x2 );
- return ublas::norm_2( (x2 - x1)/dx_ );
- }
-
-
- /**
- * @brief Makes the first guess. After this call the Newton method.
- */
- void correction_step( )
- {
- // Get the jacobian at current point. Notice that in this method, we
- // don't have to compute inverse of jacobian
-
- vector_type direction( size_ );
-
- // Now take the largest step possible such that the value of system at
- // (x_ - step ) is lower than the value of system as x_.
- vector_type nextState( size_ );
-
- apply();
-
- unsigned int i = 0;
-
- double factor = 1e-2;
- while( true )
- {
- i += 1;
- compute_jacobians( x_, false );
- // Make a move in either side of direction. In whichever direction
- // the function decreases.
- direction = ublas::prod( J_, f_ );
- nextState = x_ - factor * direction;
- if( ublas::norm_2( compute_at( nextState ) ) >= ublas::norm_2(compute_at(x_)))
- factor = factor / 2.0;
- else
- {
- cerr << "Correction term applied ";
- x_ = nextState;
- apply();
- break;
- }
-
- if ( i > 20 )
- break;
- }
- }
-
-public:
- const size_t size_;
-
- double dx_;
-
- vector_type f_;
- vector_type x_;
- vector_type slopes_;
- matrix_type J_;
- matrix_type invJ_;
-
- bool is_jacobian_valid_;
- bool is_f_positive_;
-
- // These vector keeps the temporary state computation.
- vector_type x2, x1;
-
- ReacInfo ri;
-};
diff --git a/moose-core/ksolve/VoxelPools.cpp b/moose-core/ksolve/VoxelPools.cpp
index 417c4b4316e11cf5d1ed267e6801c4e9a6a85d8d..d1bd615f8eac52cf7bcc5e02989732c720fc0d3f 100644
--- a/moose-core/ksolve/VoxelPools.cpp
+++ b/moose-core/ksolve/VoxelPools.cpp
@@ -132,7 +132,15 @@ void VoxelPools::advance( const ProcInfo* p )
double absTol = sys_.epsAbs;
double relTol = sys_.epsRel;
- double fixedDt = 0.01;
+
+
+ /**
+ * @brief Default step size for fixed size iterator.
+ * FIXME/TODO: I am not sure if this is a right value to pick by default. May be
+ * user should provide the stepping size when using fixed dt. This feature
+ * can be incredibly useful on large system.
+ */
+ const double fixedDt = 0.1;
if( sys_.method == "rk2" )
odeint::integrate_const( rk_midpoint_stepper_type_()
diff --git a/moose-core/ksolve/VoxelPoolsBase.cpp b/moose-core/ksolve/VoxelPoolsBase.cpp
index 14db1cc6b6469cadd992f832844505b4255d7c31..ecc0bab62fb8c8e9d1218d91353cd7ca1f16c88f 100644
--- a/moose-core/ksolve/VoxelPoolsBase.cpp
+++ b/moose-core/ksolve/VoxelPoolsBase.cpp
@@ -28,7 +28,7 @@ VoxelPoolsBase::VoxelPoolsBase()
S_(1),
Sinit_(1),
volume_(1.0)
-{;}
+{ ; }
VoxelPoolsBase::~VoxelPoolsBase()
{}
@@ -39,13 +39,13 @@ VoxelPoolsBase::~VoxelPoolsBase()
/// Using the computed array sizes, now allocate space for them.
void VoxelPoolsBase::resizeArrays( unsigned int totNumPools )
{
- S_.resize( totNumPools, 0.0 );
- Sinit_.resize( totNumPools, 0.0);
+ S_.resize( totNumPools, 0.0 );
+ Sinit_.resize( totNumPools, 0.0);
}
void VoxelPoolsBase::reinit()
{
- S_ = Sinit_;
+ S_ = Sinit_;
}
//////////////////////////////////////////////////////////////
diff --git a/moose-core/pymoose/CMakeLists.txt b/moose-core/pymoose/CMakeLists.txt
index bb369b44fcb3081bb18fe65d9fc494915d40cf79..e9136a08fe633ab056385e78c14a6a1f306bc7ee 100644
--- a/moose-core/pymoose/CMakeLists.txt
+++ b/moose-core/pymoose/CMakeLists.txt
@@ -13,12 +13,15 @@ set(PYMOOSE_SRCS
add_library( _moose MODULE ${PYMOOSE_SRCS} )
set(PYMOOSE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/python/moose")
-EXEC_PROGRAM(${PYTHON_EXECUTABLE}
- ARGS "-c 'try: import importlib.machinery; print(importlib.machinery.EXTENSION_SUFFIXES[0])
-except Exception: pass'"
- OUTPUT_VARIABLE PYTHON_SO_EXTENSION
- )
-message( STATUS "Python so extension ${PYTHON_SO_EXTENSION}" )
+
+find_package( PythonInterp REQUIRED )
+
+#execute_process(COMMAND
+# ${PYTHON_EXECUTABLE} "-c 'try: import importlib.machinery; print(importlib.machinery.EXTENSION_SUFFIXES[0])
+#except Exception: pass'"
+# OUTPUT_VARIABLE PYTHON_SO_EXTENSION
+# )
+#message( STATUS "Python so extension ${PYTHON_SO_EXTENSION}" )
find_package(NumPy REQUIRED)
include_directories(${NUMPY_INCLUDE_DIRS})
diff --git a/moose-core/pymoose/moosemodule.cpp b/moose-core/pymoose/moosemodule.cpp
index b5476e3e49c5331b2f5a28c768b3e7bd388cb9f6..b0653fc0fa99e1f4721c656b33895c733dbf09d4 100644
--- a/moose-core/pymoose/moosemodule.cpp
+++ b/moose-core/pymoose/moosemodule.cpp
@@ -907,7 +907,7 @@ const map<string, string>& get_field_alias()
*/
vector <string> setup_runtime_env()
{
- const map<string, string>& argmap = getArgMap();
+ const map<string, string>& argmap = moose::getArgMap();
vector<string> args;
args.push_back("moose");
map<string, string>::const_iterator it;
diff --git a/moose-core/python/moose/SBML/__init__.py b/moose-core/python/moose/SBML/__init__.py
new file mode 100755
index 0000000000000000000000000000000000000000..a3c3042fec17325167793905370ccea75c863b6b
--- /dev/null
+++ b/moose-core/python/moose/SBML/__init__.py
@@ -0,0 +1,4 @@
+from writeSBML import mooseWriteSBML
+from readSBML import mooseReadSBML
+
+__all__ = ["mooseWriteSBML","mooseReadSBML"]
diff --git a/moose-core/python/moose/SBML/readSBML.py b/moose-core/python/moose/SBML/readSBML.py
new file mode 100644
index 0000000000000000000000000000000000000000..08055a6002ab2387a935f08d22322c3dec57d851
--- /dev/null
+++ b/moose-core/python/moose/SBML/readSBML.py
@@ -0,0 +1,643 @@
+'''
+*******************************************************************
+ * File: readSBML.py
+ * Description:
+ * Author: HarshaRani
+ * E-mail: hrani@ncbs.res.in
+ ********************************************************************/
+/**********************************************************************
+** This program is part of 'MOOSE', the
+** Messaging Object Oriented Simulation Environment,
+** also known as GENESIS 3 base code.
+** copyright (C) 2003-2016 Upinder S. Bhalla. and NCBS
+Created : Thu May 12 10:19:00 2016(+0530)
+Version
+Last-Updated:
+ By:
+**********************************************************************/
+/****************************
+
+'''
+
+import sys
+import os.path
+import collections
+from moose import *
+import libsbml
+
+'''
+ TODO in
+ -Compartment
+ --Need to add group
+ --Need to deal with compartment outside
+ -Molecule
+ -- Need to add group
+ -- mathML only AssisgmentRule is taken partly I have checked addition and multiplication,
+ --, need to do for other calculation.
+ -- In Assisgment rule one of the variable is a function, in moose since assignment is done using function,
+ function can't get input from another function (model 000740 in l3v1)
+ -Loading Model from SBML
+ --Tested 1-30 testcase example model provided by l3v1 and l2v4 std.
+ ---These are the models that worked (sbml testcase)1-6,10,14-15,17-21,23-25,34,35,58
+ ---Need to check
+ ----what to do when boundarycondition is true i.e.,
+ differential equation derived from the reaction definitions
+ should not be calculated for the species(7-9,11-13,16)
+ ----kineticsLaw, Math fun has fraction,ceiling,reminder,power 28etc.
+ ----Events to be added 26
+ ----initial Assisgment for compartment 27
+ ----when stoichiometry is rational number 22
+ ---- For Michaelis Menten kinetics km is not defined which is most of the case need to calculate
+'''
+
+def mooseReadSBML(filepath,loadpath):
+ print " filepath ",filepath
+ try:
+ filep = open(filepath, "r")
+ document = libsbml.readSBML(filepath)
+ num_errors = document.getNumErrors()
+ if ( num_errors > 0 ):
+ print("Encountered the following SBML errors:" );
+ document.printErrors();
+ return moose.element('/');
+ else:
+ level = document.getLevel();
+ version = document.getVersion();
+ print("\n" + "File: " + filepath + " (Level " + str(level) + ", version " + str(version) + ")" );
+ model = document.getModel();
+ if (model == None):
+ print("No model present." );
+ return moose.element('/');
+ else:
+ print " model ",model
+ print("functionDefinitions: " + str(model.getNumFunctionDefinitions()) );
+ print(" unitDefinitions: " + str(model.getNumUnitDefinitions()) );
+ print(" compartmentTypes: " + str(model.getNumCompartmentTypes()) );
+ print(" specieTypes: " + str(model.getNumSpeciesTypes()) );
+ print(" compartments: " + str(model.getNumCompartments()) );
+ print(" species: " + str(model.getNumSpecies()) );
+ print(" parameters: " + str(model.getNumParameters()) );
+ print(" initialAssignments: " + str(model.getNumInitialAssignments()) );
+ print(" rules: " + str(model.getNumRules()) );
+ print(" constraints: " + str(model.getNumConstraints()) );
+ print(" reactions: " + str(model.getNumReactions()) );
+ print(" events: " + str(model.getNumEvents()) );
+ print("\n");
+
+ if (model.getNumCompartments() == 0):
+ return moose.element('/')
+ else:
+ baseId = moose.Neutral(loadpath)
+ #All the model will be created under model as a thumbrule
+ basePath = moose.Neutral(baseId.path+'/model')
+ #Map Compartment's SBML id as key and value is list of[ Moose ID and SpatialDimensions ]
+ comptSbmlidMooseIdMap = {}
+ print ": ",basePath.path
+ globparameterIdValue = {}
+ modelAnnotaInfo = {}
+ mapParameter(model,globparameterIdValue)
+ errorFlag = createCompartment(basePath,model,comptSbmlidMooseIdMap)
+ if errorFlag:
+ specInfoMap = {}
+ errorFlag = createSpecies(basePath,model,comptSbmlidMooseIdMap,specInfoMap)
+ if errorFlag:
+ errorFlag = createRules(model,specInfoMap,globparameterIdValue)
+ if errorFlag:
+ errorFlag = createReaction(model,specInfoMap,modelAnnotaInfo)
+ if not errorFlag:
+ print " errorFlag ",errorFlag
+ #Any time in the middle if SBML does not read then I delete everything from model level
+ #This is important as while reading in GUI the model will show up untill built which is not correct
+ print "Deleted rest of the model"
+ moose.delete(basePath)
+ return baseId;
+
+
+ except IOError:
+ print "File " ,filepath ," does not exist."
+ return moose.element('/')
+def setupEnzymaticReaction(enz,groupName,enzName,specInfoMap,modelAnnotaInfo):
+ enzPool = (modelAnnotaInfo[groupName]["enzyme"])
+ enzParent = specInfoMap[enzPool]["Mpath"]
+ cplx = (modelAnnotaInfo[groupName]["complex"])
+ complx = moose.element(specInfoMap[cplx]["Mpath"].path)
+
+ enzyme_ = moose.Enz(enzParent.path+'/'+enzName)
+ moose.move(complx,enzyme_)
+ moose.connect(enzyme_,"cplx",complx,"reac")
+ moose.connect(enzyme_,"enz",enzParent,"reac");
+
+ sublist = (modelAnnotaInfo[groupName]["substrate"])
+ prdlist = (modelAnnotaInfo[groupName]["product"])
+
+ for si in range(0,len(sublist)):
+ sl = sublist[si]
+ mSId =specInfoMap[sl]["Mpath"]
+ moose.connect(enzyme_,"sub",mSId,"reac")
+
+ for pi in range(0,len(prdlist)):
+ pl = prdlist[pi]
+ mPId = specInfoMap[pl]["Mpath"]
+ moose.connect(enzyme_,"prd",mPId,"reac")
+
+ if (enz.isSetNotes):
+ pullnotes(enz,enzyme_)
+
+def addSubPrd(reac,reName,type,reactSBMLIdMooseId,specInfoMap):
+ rctMapIter = {}
+
+ if (type == "sub"):
+ noplusStoichsub = 0
+ addSubinfo = collections.OrderedDict()
+ for rt in range(0,reac.getNumReactants()):
+ rct = reac.getReactant(rt)
+ sp = rct.getSpecies()
+ rctMapIter[sp] = rct.getStoichiometry()
+ noplusStoichsub = noplusStoichsub+rct.getStoichiometry()
+ for key,value in rctMapIter.items():
+ src = specInfoMap[key]["Mpath"]
+ des = reactSBMLIdMooseId[reName]["MooseId"]
+ for s in range(0,int(value)):
+ moose.connect(des, 'sub', src, 'reac', 'OneToOne')
+ addSubinfo = {"nSub" :noplusStoichsub}
+ reactSBMLIdMooseId[reName].update(addSubinfo)
+
+ else:
+ noplusStoichprd = 0
+ addPrdinfo = collections.OrderedDict()
+ for rt in range(0,reac.getNumProducts()):
+ rct = reac.getProduct(rt)
+ sp = rct.getSpecies()
+ rctMapIter[sp] = rct.getStoichiometry()
+ noplusStoichprd = noplusStoichprd+rct.getStoichiometry()
+
+ for key,values in rctMapIter.items():
+ #src ReacBase
+ src = reactSBMLIdMooseId[reName]["MooseId"]
+ des = specInfoMap[key]["Mpath"]
+ for i in range(0,int(values)):
+ moose.connect(src, 'prd', des, 'reac', 'OneToOne')
+ addPrdinfo = {"nPrd": noplusStoichprd}
+ reactSBMLIdMooseId[reName].update(addPrdinfo)
+
+def populatedict(annoDict,label,value):
+ if annoDict.has_key(label):
+ annoDict.setdefault(label,[])
+ annoDict[label].update({value})
+ else:
+ annoDict[label]= {value}
+
+def getModelAnnotation(obj,modelAnnotaInfo):
+ name = obj.getId()
+ name = name.replace(" ","_space_")
+ #modelAnnotaInfo= {}
+ annotateMap = {}
+ if (obj.getAnnotation() != None):
+ annoNode = obj.getAnnotation()
+ for ch in range(0,annoNode.getNumChildren()):
+ childNode = annoNode.getChild(ch)
+ if (childNode.getPrefix() == "moose" and childNode.getName() == "EnzymaticReaction"):
+ sublist = []
+ for gch in range(0,childNode.getNumChildren()):
+ grandChildNode = childNode.getChild(gch)
+ nodeName = grandChildNode.getName()
+ nodeValue = ""
+ if (grandChildNode.getNumChildren() == 1):
+ nodeValue = grandChildNode.getChild(0).toXMLString()
+ else:
+ print "Error: expected exactly ONE child of ", nodeName
+
+ if nodeName == "enzyme":
+ populatedict(annotateMap,"enzyme",nodeValue)
+
+ elif nodeName == "complex":
+ populatedict(annotateMap,"complex" ,nodeValue)
+ elif ( nodeName == "substrates"):
+ populatedict(annotateMap,"substrates" ,nodeValue)
+ elif ( nodeName == "product" ):
+ populatedict(annotateMap,"product" ,nodeValue)
+ elif ( nodeName == "groupName" ):
+ populatedict(annotateMap,"grpName" ,nodeValue)
+ elif ( nodeName == "stage" ):
+ populatedict(annotateMap,"stage" ,nodeValue)
+ elif ( nodeName == "Group" ):
+ populatedict(annotateMap,"group" ,nodeValue)
+ elif ( nodeName == "xCord" ):
+ populatedict(annotateMap,"xCord" ,nodeValue)
+ elif ( nodeName == "yCord" ):
+ populatedict(annotateMap,"yCord" ,nodeValue)
+ groupName = ""
+ if annotateMap.has_key('grpName'):
+ groupName = list(annotateMap["grpName"])[0]
+ if list(annotateMap["stage"])[0] == '1':
+ if modelAnnotaInfo.has_key(groupName):
+ modelAnnotaInfo[groupName].update (
+ {"enzyme" : list(annotateMap["enzyme"])[0],
+ "stage" : list(annotateMap["stage"])[0],
+ "substrate" : list(annotateMap["substrates"])
+ }
+ )
+ else:
+ modelAnnotaInfo[groupName]= {
+ "enzyme" : list(annotateMap["enzyme"])[0],
+ "stage" : list(annotateMap["stage"])[0],
+ "substrate" : list(annotateMap["substrates"])
+ #"group" : list(annotateMap["Group"])[0],
+ #"xCord" : list(annotateMap["xCord"])[0],
+ #"yCord" : list(annotateMap["yCord"]) [0]
+ }
+
+ elif list(annotateMap["stage"])[0] == '2':
+ if modelAnnotaInfo.has_key(groupName):
+ stage = int(modelAnnotaInfo[groupName]["stage"])+int(list(annotateMap["stage"])[0])
+ modelAnnotaInfo[groupName].update (
+ {"complex" : list(annotateMap["complex"])[0],
+ "product" : list(annotateMap["product"]),
+ "stage" : [stage]
+ }
+ )
+ else:
+ modelAnnotaInfo[groupName]= {
+ "complex" : list(annotateMap["complex"])[0],
+ "product" : list(annotateMap["product"]),
+ "stage" : [stage]
+ }
+ return(groupName)
+
+
+def createReaction(model,specInfoMap,modelAnnotaInfo):
+ # print " reaction "
+ # Things done for reaction
+ # --Reaction is not created, if substrate and product is missing
+ # --Reaction is created under first substrate's compartment if substrate not found then product
+ # --Reaction is created if substrate or product is missing, but while run time in GUI atleast I have stopped
+ #ToDo
+ # -- I need to check here if any substance/product is if ( constant == true && bcondition == false)
+ # cout <<"The species "<< name << " should not appear in reactant or product as per sbml Rules"<< endl;
+
+ errorFlag = True
+ reactSBMLIdMooseId = {}
+
+ for ritem in range(0,model.getNumReactions()):
+ reactionCreated = False
+ groupName = ""
+ reac = model.getReaction( ritem )
+ if ( reac.isSetId() ):
+ rId = reac.getId()
+ if ( reac.isSetName() ):
+ rName = reac.getName()
+ rName = rName.replace(" ","_space_")
+ if not( rName ):
+ rName = rId
+ rev = reac.getReversible()
+ fast = reac.getFast()
+ if ( fast ):
+ print " warning: for now fast attribute is not handled \"", rName,"\""
+ if (reac.getAnnotation() != None):
+ groupName = getModelAnnotation(reac,modelAnnotaInfo)
+
+ if (groupName != "" and list(modelAnnotaInfo[groupName]["stage"])[0] == 3):
+ setupEnzymaticReaction(reac,groupName,rName,specInfoMap,modelAnnotaInfo)
+
+ elif(groupName == ""):
+ numRcts = reac.getNumReactants()
+ numPdts = reac.getNumProducts()
+ nummodifiers = reac.getNumModifiers()
+
+ if not (numRcts and numPdts):
+ print rName," : Substrate and Product is missing, we will be skiping creating this reaction in MOOSE"
+
+ elif (reac.getNumModifiers() > 0):
+ reactionCreated = setupMMEnzymeReaction(reac,rName,specInfoMap,reactSBMLIdMooseId)
+ print " reactionCreated after enz ",reactionCreated
+
+ elif (numRcts):
+ # In moose, reactions compartment are decided from first Substrate compartment info
+ # substrate is missing then check for product
+ if (reac.getNumReactants()):
+ react = reac.getReactant(0)
+ sp = react.getSpecies()
+ speCompt = specInfoMap[sp]["comptId"].path
+ reaction_ = moose.Reac(speCompt+'/'+rName)
+ reactionCreated = True
+ reactSBMLIdMooseId[rName] = {"MooseId" : reaction_ , "className ": "reaction"}
+ elif (numPdts):
+ # In moose, reactions compartment are decided from first Substrate compartment info
+ # substrate is missing then check for product
+ if (reac.getNumProducts()):
+ react = reac.getProducts(0)
+ sp = react.getSpecies()
+ speCompt = specInfoMap[sp]["comptId"].path
+ reaction_ = moose.Reac(speCompt+'/'+rName)
+ reactionCreated = True
+ reactSBMLIdMooseId[rName] = {"MooseId":reaction_}
+
+ if reactionCreated:
+ if (reac.isSetNotes):
+ pullnotes(reac,reaction_)
+ addSubPrd(reac,rName,"sub",reactSBMLIdMooseId,specInfoMap)
+ addSubPrd(reac,rName,"prd",reactSBMLIdMooseId,specInfoMap)
+ # print "react ",reactSBMLIdMooseId
+ return errorFlag
+
+def getMembers(node,ruleMemlist):
+ if node.getType() == libsbml.AST_PLUS:
+ if node.getNumChildren() == 0:
+ print ("0")
+ return
+ getMembers(node.getChild(0),ruleMemlist)
+ for i in range(1,node.getNumChildren()):
+ # addition
+ getMembers(node.getChild(i),ruleMemlist)
+ elif node.getType() == libsbml.AST_REAL:
+ #This will be constant
+ pass
+ elif node.getType() == libsbml.AST_NAME:
+ #This will be the ci term"
+ ruleMemlist.append(node.getName())
+
+ elif node.getType() == libsbml.AST_TIMES:
+ if node.getNumChildren() == 0:
+ print ("0")
+ return
+ getMembers(node.getChild(0),ruleMemlist)
+ for i in range(1,node.getNumChildren()):
+ # Multiplication
+ getMembers(node.getChild(i),ruleMemlist)
+ else:
+ print " this case need to be handled"
+
+def createRules(model,specInfoMap,globparameterIdValue):
+ for r in range(0,model.getNumRules()):
+ rule = model.getRule(r)
+ if (rule.isAssignment()):
+ rule_variable = rule.getVariable();
+ poolList = specInfoMap[rule_variable]["Mpath"].path
+ funcId = moose.Function(poolList+'/func')
+ moose.connect( funcId, 'valueOut', poolList ,'setN' )
+ ruleMath = rule.getMath()
+ ruleMemlist = []
+ speFunXterm = {}
+ getMembers(ruleMath,ruleMemlist)
+ for i in ruleMemlist:
+ if (specInfoMap.has_key(i)):
+ specMapList = specInfoMap[i]["Mpath"]
+ numVars = funcId.numVars
+ x = funcId.path+'/x['+str(numVars)+']'
+ speFunXterm[i] = 'x'+str(numVars)
+ moose.connect(specMapList , 'nOut', x, 'input' )
+ funcId.numVars = numVars +1
+ elif not(globparameterIdValue.has_key(i)):
+ print "check the variable type ",i
+
+ exp = rule.getFormula()
+ for mem in ruleMemlist:
+ if ( specInfoMap.has_key(mem)):
+ exp1 = exp.replace(mem,str(speFunXterm[mem]))
+ exp = exp1
+ elif( globparameterIdValue.has_key(mem)):
+ exp1 = exp.replace(mem,str(globparameterIdValue[mem]))
+ exp = exp1
+ else:
+ print "Math expression need to be checked"
+ funcId.expr = exp.strip(" \t\n\r")
+ return True
+
+ elif( rule.isRate() ):
+ print "Warning : For now this \"",rule.getVariable(), "\" rate Rule is not handled in moose "
+ return False
+
+ elif ( rule.isAlgebraic() ):
+ print "Warning: For now this " ,rule.getVariable()," Algebraic Rule is not handled in moose"
+ return False
+ return True
+
+def pullnotes(sbmlId,mooseId):
+ if sbmlId.getNotes() != None:
+ tnodec = ((sbmlId.getNotes()).getChild(0)).getChild(0)
+ notes = tnodec.getCharacters()
+ notes = notes.strip(' \t\n\r')
+ objPath = mooseId.path+"/info"
+ if not moose.exists(objPath):
+ objInfo = moose.Annotator(mooseId.path+'/info')
+ else:
+ objInfo = moose.element(mooseId.path+'/info')
+ objInfo.notes = notes
+
+def createSpecies(basePath,model,comptSbmlidMooseIdMap,specInfoMap):
+ # ToDo:
+ # - Need to add group name if exist in pool
+ # - Notes
+ # print "species "
+ if not (model.getNumSpecies()):
+ return False
+ else:
+ for sindex in range(0,model.getNumSpecies()):
+ spe = model.getSpecies(sindex)
+ sName = None
+ sId = spe.getId()
+
+ if spe.isSetName():
+ sName = spe.getName()
+ sName = sName.replace(" ","_space_")
+
+ if spe.isSetCompartment():
+ comptId = spe.getCompartment()
+
+ if not( sName ):
+ sName = sId
+
+ constant = spe.getConstant()
+ boundaryCondition = spe.getBoundaryCondition()
+ comptEl = comptSbmlidMooseIdMap[comptId]["MooseId"].path
+ hasonlySubUnit = spe.getHasOnlySubstanceUnits();
+ # "false": is {unit of amount}/{unit of size} (i.e., concentration or density).
+ # "true": then the value is interpreted as having a unit of amount only.
+
+ if (boundaryCondition):
+ poolId = moose.BufPool(comptEl+'/'+sName)
+ else:
+ poolId = moose.Pool(comptEl+'/'+sName)
+
+ if (spe.isSetNotes):
+ pullnotes(spe,poolId)
+
+ specInfoMap[sId] = {"Mpath" : poolId, "const" : constant, "bcondition" : boundaryCondition, "hassubunit" : hasonlySubUnit, "comptId" : comptSbmlidMooseIdMap[comptId]["MooseId"]}
+ initvalue = 0.0
+ unitfactor,unitset,unittype = transformUnit(spe,hasonlySubUnit)
+ if hasonlySubUnit == True:
+ if spe.isSetInitialAmount():
+ initvalue = spe.getInitialAmount()
+ # populating nInit, will automatically calculate the concInit.
+ if not (unitset):
+ # if unit is not set,
+ # default unit is assumed as Mole in SBML
+ unitfactor = pow(6.0221409e23,1)
+ unittype = "Mole"
+
+ initvalue = initvalue * unitfactor
+ elif spe.isSetInitialConcentration():
+ initvalue = spe.getInitialConcentration()
+ print " Since hasonlySubUnit is true and concentration is set units are not checked"
+ poolId.nInit = initvalue
+
+ elif hasonlySubUnit == False:
+ #ToDo : check 00976
+ if spe.isSetInitialAmount():
+ initvalue = spe.getInitialAmount()
+ #initAmount is set we need to convert to concentration
+ initvalue = initvalue / comptSbmlidMooseIdMap[comptId]["size"]
+
+ elif spe.isSetInitialConcentration():
+ initvalue = spe.getInitialConcentration()
+ if not unitset:
+ #print " unit is not set"
+ unitfactor = power(10,-3)
+
+ initvalue = initvalue * unitfactor
+ poolId.concInit = initvalue
+ else:
+ nr = model.getNumRules()
+ found = False
+ for nrItem in range(0,nr):
+ rule = model.getRule(nrItem)
+ assignRule = rule.isAssignment()
+ if ( assignRule ):
+ rule_variable = rule.getVariable()
+ if (rule_variable == sId):
+ found = True
+ break
+ if not (found):
+ print "Invalid SBML: Either initialConcentration or initialAmount must be set or it should be found in assignmentRule but non happening for ",sName
+ return False
+ return True
+
+def transformUnit(unitForObject,hasonlySubUnit=False):
+ #print "unit ",UnitDefinition.printUnits(unitForObject.getDerivedUnitDefinition())
+ unitset = False
+ unittype = None
+ if (unitForObject.getDerivedUnitDefinition()):
+ unit = (unitForObject.getDerivedUnitDefinition())
+ unitnumber = int(unit.getNumUnits())
+ if unitnumber > 0:
+ for ui in range(0,unit.getNumUnits()):
+ lvalue = 1.0
+ unitType = unit.getUnit(ui)
+ if( unitType.isLitre()):
+ exponent = unitType.getExponent()
+ multiplier = unitType.getMultiplier()
+ scale = unitType.getScale()
+ offset = unitType.getOffset()
+ #units for compartment is Litre but MOOSE compartment is m3
+ scale = scale-3
+ lvalue *= pow( multiplier * pow(10.0,scale), exponent ) + offset;
+ unitset = True
+ unittype = "Litre"
+
+ elif( unitType.isMole()):
+ exponent = unitType.getExponent()
+ multiplier = unitType.getMultiplier()
+ scale = unitType.getScale()
+ offset = unitType.getOffset()
+ #if hasOnlySubstanceUnit = True, then assuming Amount
+ if hasonlySubUnit == True:
+ lvalue *= pow(multiplier * pow(10.0,scale),exponent) + offset
+ #If SBML units are in mole then convert to number by multiplying with avogadro's number
+ lvalue = lvalue * pow(6.0221409e23,1)
+
+ elif hasonlySubUnit == False:
+ #Pool units are in mM, so to scale adding +3 to convert to m
+ lvalue *= pow( multiplier * pow(10.0,scale+3), exponent ) + offset;
+ unitset = True
+ unittype = "Mole"
+
+ elif( unitType.isItem()):
+ exponent = unitType.getExponent()
+ multiplier = unitType.getMultiplier()
+ scale = unitType.getScale()
+ offset = unitType.getOffset()
+ #if hasOnlySubstanceUnit = True, then assuming Amount
+ if hasonlySubUnit == True:
+ #If SBML units are in Item then amount is populate as its
+ lvalue *= pow( multiplier * pow(10.0,scale), exponent ) + offset;
+ if hasonlySubUnit == False:
+ # hasonlySubUnit is False, which is assumed concentration,
+ # Here Item is converted to mole by dividing by avogadro and at initiavalue divided by volume"
+ lvalue *= pow( multiplier * pow(10.0,scale), exponent ) + offset;
+ lvalue = lvalue/pow(6.0221409e23,1)
+ unitset = True
+ unittype = "Item"
+ else:
+ lvalue = 1.0
+ print " end of the func lvaue ",lvalue
+ return (lvalue,unitset,unittype)
+def createCompartment(basePath,model,comptSbmlidMooseIdMap):
+ #ToDoList : Check what should be done for the spaitialdimension is 2 or 1, area or length
+ if not(model.getNumCompartments()):
+ return False
+ else:
+ for c in range(0,model.getNumCompartments()):
+ compt = model.getCompartment(c)
+ # print("Compartment " + str(c) + ": "+ UnitDefinition.printUnits(compt.getDerivedUnitDefinition()))
+ msize = 0.0
+ unitfactor = 1.0
+ sbmlCmptId = None
+ name = None
+
+ if ( compt.isSetId() ):
+ sbmlCmptId = compt.getId()
+
+ if ( compt.isSetName() ):
+ name = compt.getName()
+ name = name.replace(" ","_space")
+
+ if ( compt.isSetOutside() ):
+ outside = compt.getOutside()
+
+ if ( compt.isSetSize() ):
+ msize = compt.getSize()
+ if msize == 1:
+ print "Compartment size is 1"
+
+ dimension = compt.getSpatialDimensions();
+ if dimension == 3:
+ unitfactor,unitset, unittype = transformUnit(compt)
+
+ else:
+ print " Currently we don't deal with spatial Dimension less than 3 and unit's area or length"
+ return False
+
+ if not( name ):
+ name = sbmlCmptId
+
+ mooseCmptId = moose.CubeMesh(basePath.path+'/'+name)
+ mooseCmptId.volume = (msize*unitfactor)
+ comptSbmlidMooseIdMap[sbmlCmptId]={"MooseId": mooseCmptId, "spatialDim":dimension, "size" : msize}
+ return True
+def mapParameter(model,globparameterIdValue):
+ for pm in range(0,model.getNumParameters()):
+ prm = model.getParameter( pm );
+ if ( prm.isSetId() ):
+ parid = prm.getId()
+ value = 0.0;
+ if ( prm.isSetValue() ):
+ value = prm.getValue()
+ globparameterIdValue[parid] = value
+
+if __name__ == "__main__":
+
+ filepath = sys.argv[1]
+ path = sys.argv[2]
+
+ f = open(filepath, 'r')
+
+ if path == '':
+ loadpath = filepath[filepath.rfind('/'):filepath.find('.')]
+ else:
+ loadpath = path
+
+ read = mooseReadSBML(filepath,loadpath)
+ if read:
+ print " Read to path",loadpath
+ else:
+ print " could not read SBML to MOOSE"
diff --git a/moose-core/python/moose/SBML/writeSBML.py b/moose-core/python/moose/SBML/writeSBML.py
new file mode 100644
index 0000000000000000000000000000000000000000..b810c7bb17dcceafdf9b5928208565bd4a5e353b
--- /dev/null
+++ b/moose-core/python/moose/SBML/writeSBML.py
@@ -0,0 +1,734 @@
+'''
+*******************************************************************
+ * File: writeSBML.py
+ * Description:
+ * Author: HarshaRani
+ * E-mail: hrani@ncbs.res.in
+ ********************************************************************/
+/**********************************************************************
+** This program is part of 'MOOSE', the
+** Messaging Object Oriented Simulation Environment,
+** also known as GENESIS 3 base code.
+** copyright (C) 2003-2016 Upinder S. Bhalla. and NCBS
+Created : Friday May 27 12:19:00 2016(+0530)
+Version
+Last-Updated:
+ By:
+**********************************************************************/
+/****************************
+
+'''
+from moose import *
+from libsbml import *
+import re
+from collections import Counter
+#from moose import wildcardFind, element, loadModel, ChemCompt, exists, Annotator, Pool, ZombiePool,PoolBase,CplxEnzBase,Function,ZombieFunction
+
+#ToDo:
+# Table should be written
+# Group's should be added
+# x and y cordinates shd be added if exist
+
+def mooseWriteSBML(modelpath,filename):
+ sbmlDoc = SBMLDocument(3, 1)
+ filepath,filenameExt = os.path.split(filename)
+ if filenameExt.find('.') != -1:
+ filename = filenameExt[:filenameExt.find('.')]
+ else:
+ filename = filenameExt
+
+ #validatemodel
+ sbmlOk = False
+ global spe_constTrue
+ spe_constTrue = []
+ global nameList_
+ nameList_ = []
+
+ xmlns = XMLNamespaces()
+ xmlns.add("http://www.sbml.org/sbml/level3/version1")
+ xmlns.add("http://www.moose.ncbs.res.in","moose")
+ xmlns.add("http://www.w3.org/1999/xhtml","xhtml")
+ sbmlDoc.setNamespaces(xmlns)
+ cremodel_ = sbmlDoc.createModel()
+ cremodel_.setId(filename)
+ cremodel_.setTimeUnits("second")
+ cremodel_.setExtentUnits("substance")
+ cremodel_.setSubstanceUnits("substance")
+
+ writeUnits(cremodel_)
+ modelAnno = writeSimulationAnnotation(modelpath)
+ if modelAnno:
+ cremodel_.setAnnotation(modelAnno)
+ compartexist = writeCompt(modelpath,cremodel_)
+ species = writeSpecies(modelpath,cremodel_,sbmlDoc)
+ if species:
+ writeFunc(modelpath,cremodel_)
+ writeReac(modelpath,cremodel_)
+ writeEnz(modelpath,cremodel_)
+
+ consistencyMessages = ""
+ SBMLok = validateModel( sbmlDoc )
+ if ( SBMLok ):
+ #filepath = '/home/harsha/Trash/python'
+ #SBMLString = writeSBMLToString(sbmlDoc)
+ writeTofile = filepath+"/"+filename+'.xml'
+ writeSBMLToFile( sbmlDoc, writeTofile)
+ return True,consistencyMessages
+
+ if ( not SBMLok ):
+ cerr << "Errors encountered " << endl;
+ return -1,consistencyMessages
+
+def writeEnz(modelpath,cremodel_):
+ for enz in wildcardFind(modelpath+'/##[ISA=EnzBase]'):
+ enzannoexist = False
+ enzGpname = " "
+ cleanEnzname = convertSpecialChar(enz.name)
+ enzSubt = ()
+
+ if moose.exists(enz.path+'/info'):
+ Anno = moose.Annotator(enz.path+'/info')
+ notesE = Anno.notes
+ element = moose.element(enz)
+ ele = getGroupinfo(element)
+ if ele.className == "Neutral":
+ enzGpname = "<moose:Group> "+ ele.name + " </moose:Group>\n"
+ enzannoexist = True
+
+ if (enz.className == "Enz" or enz.className == "ZombieEnz"):
+ enzyme = cremodel_.createReaction()
+ if notesE != "":
+ cleanNotesE= convertNotesSpecialChar(notesE)
+ notesStringE = "<body xmlns=\"http://www.w3.org/1999/xhtml\">\n \t \t"+ cleanNotesE + "\n\t </body>"
+ enzyme.setNotes(notesStringE)
+ enzyme.setId(str(idBeginWith(cleanEnzname+"_"+str(enz.getId().value)+"_"+str(enz.getDataIndex())+"_"+"Complex_formation_")))
+ enzyme.setName(cleanEnzname)
+ enzyme.setFast ( False )
+ enzyme.setReversible( True)
+ k1 = enz.k1
+ k2 = enz.k2
+ k3 = enz.k3
+
+ enzAnno ="<moose:EnzymaticReaction>\n"
+ if enzannoexist:
+ enzAnno=enzAnno + enzGpname
+ enzOut = enz.neighbors["enzOut"]
+
+ if not enzOut:
+ print " Enzyme parent missing for ",enz.name
+ else:
+ listofname(enzOut,True)
+ enzSubt = enzOut
+ for i in range(0,len(nameList_)):
+ enzAnno=enzAnno+"<moose:enzyme>"+nameList_[i]+"</moose:enzyme>\n"
+ #noofSub,sRateLaw = getSubprd(cremodel_,True,"sub",enzSub)
+ #for i in range(0,len(nameList_)):
+ # enzAnno=enzAnno+"<moose:enzyme>"+nameList_[i]+"</moose:enzyme>\n"
+ #rec_order = noofSub
+ #rate_law = "k1"+"*"+sRateLaw
+
+ enzSub = enz.neighbors["sub"]
+ if not enzSub:
+ print "Enzyme \"",enz.name,"\" substrate missing"
+ else:
+ listofname(enzSub,True)
+ enzSubt += enzSub
+ for i in range(0,len(nameList_)):
+ enzAnno= enzAnno+"<moose:substrates>"+nameList_[i]+"</moose:substrates>\n"
+ if enzSubt:
+ rate_law = "k1"
+ noofSub,sRateLaw = getSubprd(cremodel_,True,"sub",enzSubt)
+ #rec_order = rec_order + noofSub
+ rec_order = noofSub
+ rate_law = rate_law +"*"+sRateLaw
+
+
+
+ enzPrd = enz.neighbors["cplxDest"]
+ if not enzPrd:
+ print "Enzyme \"",enz.name,"\"product missing"
+ else:
+ noofPrd,sRateLaw = getSubprd(cremodel_,True,"prd",enzPrd)
+ for i in range(0,len(nameList_)):
+ enzAnno= enzAnno+"<moose:product>"+nameList_[i]+"</moose:product>\n"
+ rate_law = rate_law+ " - "+"k2"+'*'+sRateLaw
+
+ prd_order = noofPrd
+ enzAnno = enzAnno + "<moose:groupName>" + cleanEnzname + "_" + str(enz.getId().value) + "_" + str(enz.getDataIndex()) + "_" + "</moose:groupName>\n"
+ enzAnno = enzAnno+"<moose:stage>1</moose:stage>\n"
+ enzAnno = enzAnno+ "</moose:EnzymaticReaction>"
+ enzyme.setAnnotation(enzAnno)
+ kl = enzyme.createKineticLaw()
+ kl.setFormula( rate_law )
+ punit = parmUnit( prd_order-1, cremodel_ )
+ printParameters( kl,"k2",k2,punit )
+
+ unit = parmUnit( rec_order-1, cremodel_)
+ printParameters( kl,"k1",k1,unit )
+ enzyme = cremodel_.createReaction()
+ enzyme.setId(str(idBeginWith(cleanEnzname+"_"+str(enz.getId().value)+"_"+str(enz.getDataIndex())+"_"+"Product_formation_")))
+ enzyme.setName(cleanEnzname)
+ enzyme.setFast ( False )
+ enzyme.setReversible( False )
+ enzAnno2 = "<moose:EnzymaticReaction>"
+
+ enzSub = enz.neighbors["cplxDest"]
+ if not enzSub:
+ print " complex missing from ",enz.name
+ else:
+ noofSub,sRateLaw = getSubprd(cremodel_,True,"sub",enzSub)
+ for i in range(0,len(nameList_)):
+ enzAnno2 = enzAnno2+"<moose:complex>"+nameList_[i]+"</moose:complex>\n"
+
+ enzEnz = enz.neighbors["enzOut"]
+ if not enzEnz:
+ print "Enzyme parent missing for ",enz.name
+ else:
+ noofEnz,sRateLaw1 = getSubprd(cremodel_,True,"prd",enzEnz)
+ for i in range(0,len(nameList_)):
+ enzAnno2 = enzAnno2+"<moose:enzyme>"+nameList_[i]+"</moose:enzyme>\n"
+ enzPrd = enz.neighbors["prd"]
+ if enzPrd:
+ noofprd,sRateLaw2 = getSubprd(cremodel_,True,"prd",enzPrd)
+ else:
+ print "Enzyme \"",enz.name, "\" product missing"
+ for i in range(0,len(nameList_)):
+ enzAnno2 = enzAnno2+"<moose:product>"+nameList_[i]+"</moose:product>\n"
+ enzAnno2 += "<moose:groupName>"+ cleanEnzname + "_" + str(enz.getId().value) + "_" + str(enz.getDataIndex())+"_" +"</moose:groupName>\n";
+ enzAnno2 += "<moose:stage>2</moose:stage> \n";
+ enzAnno2 += "</moose:EnzymaticReaction>";
+ enzyme.setAnnotation( enzAnno2 );
+
+ enzrate_law = "k3" + '*'+sRateLaw;
+ kl = enzyme.createKineticLaw();
+ kl.setFormula( enzrate_law );
+ unit = parmUnit(noofPrd-1 ,cremodel_)
+ printParameters( kl,"k3",k3,unit );
+
+ elif(enz.className == "MMenz" or enz.className == "ZombieMMenz"):
+ enzyme = cremodel_.createReaction()
+
+ if notesE != "":
+ cleanNotesE= convertNotesSpecialChar(notesE)
+ notesStringE = "<body xmlns=\"http://www.w3.org/1999/xhtml\">\n \t \t"+ cleanNotesE + "\n\t </body>"
+ enzyme.setNotes(notesStringE)
+ enzyme.setId(str(idBeginWith(cleanEnzname+"_"+str(enz.getId().value)+"_"+str(enz.getDataIndex())+"_")))
+ enzyme.setName(cleanEnzname)
+ enzyme.setFast ( False )
+ enzyme.setReversible( True)
+ if enzannoexist:
+ enzAnno = "<moose:EnzymaticReaction>\n" + enzGpname + "</moose:EnzymaticReaction>";
+ enzyme.setAnnotation(enzAnno)
+ Km = enz.numKm
+ kcat = enz.kcat
+ enzSub = enz.neighbors["sub"]
+ noofSub,sRateLawS = getSubprd(cremodel_,False,"sub",enzSub)
+ #sRate_law << rate_law.str();
+ #Modifier
+ enzMod = enz.neighbors["enzDest"]
+ noofMod,sRateLawM = getSubprd(cremodel_,False,"enz",enzMod)
+ enzPrd = enz.neighbors["prd"]
+ noofPrd,sRateLawP = getSubprd(cremodel_,False,"prd",enzPrd)
+ kl = enzyme.createKineticLaw()
+ fRate_law ="kcat *" + sRateLawS + "*" + sRateLawM + "/" + "(" + "Km" + "+" +sRateLawS +")"
+ kl.setFormula(fRate_law)
+ kl.setNotes("<body xmlns=\"http://www.w3.org/1999/xhtml\">\n\t\t" + fRate_law + "\n \t </body>")
+ printParameters( kl,"Km",Km,"substance" )
+ kcatUnit = parmUnit( 0,cremodel_ )
+ printParameters( kl,"kcat",kcat,kcatUnit )
+
+def printParameters( kl, k, kvalue, unit ):
+ para = kl.createParameter()
+ para.setId(str(idBeginWith( k )))
+ para.setValue( kvalue )
+ para.setUnits( unit )
+
+def parmUnit( rct_order,cremodel_ ):
+ order = rct_order
+ if order == 0:
+ unit_stream = "per_second"
+ elif order == 1:
+ unit_stream = "per_item_per_second"
+ elif order == 2:
+ unit_stream ="per_item_sq_per_second"
+ else:
+ unit_stream = "per_item_"+str(rct_order)+"_per_second";
+
+ lud =cremodel_.getListOfUnitDefinitions();
+ flag = False;
+ for i in range( 0,len(lud)):
+ ud = lud.get(i);
+ if ( ud.getId() == unit_stream ):
+ flag = True;
+ break;
+ if ( not flag ):
+ unitdef = cremodel_.createUnitDefinition()
+ unitdef.setId( unit_stream)
+ #Create individual unit objects that will be put inside the UnitDefinition .
+ if order != 0 :
+ unit = unitdef.createUnit()
+ unit.setKind( UNIT_KIND_ITEM )
+ unit.setExponent( -order )
+ unit.setMultiplier(1)
+ unit.setScale( 0 )
+
+ unit = unitdef.createUnit();
+ unit.setKind( UNIT_KIND_SECOND );
+ unit.setExponent( -1 );
+ unit.setMultiplier( 1 );
+ unit.setScale ( 0 );
+ return unit_stream
+
+def getSubprd(cremodel_,mobjEnz,type,neighborslist):
+ if type == "sub":
+ reacSub = neighborslist
+ reacSubCou = Counter(reacSub)
+
+ #print " reacSubCou ",reacSubCou,"()",len(reacSubCou)
+ noofSub = len(reacSubCou)
+ rate_law = " "
+ if reacSub:
+ rate_law = processRateLaw(reacSubCou,cremodel_,noofSub,"sub",mobjEnz)
+ return len(reacSub),rate_law
+ else:
+ print reac.className+ " has no substrate"
+ return 0,rate_law
+ elif type == "prd":
+ reacPrd = neighborslist
+ reacPrdCou = Counter(reacPrd)
+ noofPrd = len(reacPrdCou)
+ rate_law = " "
+ if reacPrd:
+ rate_law = processRateLaw(reacPrdCou,cremodel_,noofPrd,"prd",mobjEnz)
+ return len(reacPrd),rate_law
+ elif type == "enz":
+ enzModifier = neighborslist
+ enzModCou = Counter(enzModifier)
+ noofMod = len(enzModCou)
+ rate_law = " "
+ if enzModifier:
+ rate_law = processRateLaw(enzModCou,cremodel_,noofMod,"Modifier",mobjEnz)
+ return len(enzModifier),rate_law
+
+
+def processRateLaw(objectCount,cremodel,noofObj,type,mobjEnz):
+ rate_law = ""
+ nameList_[:] = []
+ for value,count in objectCount.iteritems():
+ value = moose.element(value)
+ nameIndex = value.name+"_"+str(value.getId().value)+"_"+str(value.getDataIndex())+"_"
+ clean_name = (str(idBeginWith(convertSpecialChar(nameIndex))))
+ if mobjEnz == True:
+ nameList_.append(clean_name)
+ if type == "sub":
+ sbmlRef = cremodel.createReactant()
+ elif type == "prd":
+ sbmlRef = cremodel.createProduct()
+ elif type == "Modifier":
+ sbmlRef = cremodel.createModifier()
+ sbmlRef.setSpecies(clean_name)
+
+ if type == "sub" or type == "prd":
+ sbmlRef.setSpecies(clean_name)
+
+ sbmlRef.setStoichiometry( count)
+ if clean_name in spe_constTrue:
+ sbmlRef.setConstant(True)
+ else:
+ sbmlRef.setConstant(False)
+ if ( count == 1 ):
+ if rate_law == "":
+ rate_law = clean_name
+ else:
+ rate_law = rate_law+"*"+clean_name
+ else:
+ if rate_law == "":
+ rate_law = clean_name+"^"+str(count)
+ else:
+ rate_law = rate_law+"*"+clean_name + "^" + str(count)
+ return(rate_law)
+
+def listofname(reacSub,mobjEnz):
+ objectCount = Counter(reacSub)
+ nameList_[:] = []
+ for value,count in objectCount.iteritems():
+ value = moose.element(value)
+ nameIndex = value.name+"_"+str(value.getId().value)+"_"+str(value.getDataIndex())+"_"
+ clean_name = convertSpecialChar(nameIndex)
+ if mobjEnz == True:
+ nameList_.append(clean_name)
+def writeReac(modelpath,cremodel_):
+ for reac in wildcardFind(modelpath+'/##[ISA=ReacBase]'):
+ reaction = cremodel_.createReaction()
+ reacannoexist = False
+ reacGpname = " "
+ cleanReacname = convertSpecialChar(reac.name)
+ reaction.setId(str(idBeginWith(cleanReacname+"_"+str(reac.getId().value)+"_"+str(reac.getDataIndex())+"_")))
+ reaction.setName(cleanReacname)
+ Kf = reac.numKf
+ Kb = reac.numKb
+ if Kb == 0.0:
+ reaction.setReversible( False )
+ else:
+ reaction.setReversible( True )
+
+ reaction.setFast( False )
+ if moose.exists(reac.path+'/info'):
+ Anno = moose.Annotator(reac.path+'/info')
+ notesR = Anno.notes
+ if notesR != "":
+ cleanNotesR= convertNotesSpecialChar(notesR)
+ notesStringR = "<body xmlns=\"http://www.w3.org/1999/xhtml\">\n \t \t"+ cleanNotesR + "\n\t </body>"
+ reaction.setNotes(notesStringR)
+ element = moose.element(reac)
+ ele = getGroupinfo(element)
+ if ele.className == "Neutral":
+ reacGpname = "<moose:Group>"+ ele.name + "</moose:Group>\n"
+ reacannoexist = True
+ if reacannoexist :
+ reacAnno = "<moose:ModelAnnotation>\n"
+ if reacGpname:
+ reacAnno = reacAnno + reacGpname
+ reacAnno = reacAnno+ "</moose:ModelAnnotation>"
+ #s1.appendAnnotation(XMLNode.convertStringToXMLNode(speciAnno))
+ reaction.setAnnotation(reacAnno)
+
+ kl_s = sRL = pRL = ""
+
+ reacSub = reac.neighbors["sub"]
+ reacPrd = reac.neighbors["prd"]
+ if not reacSub and not reacPrd:
+ print " Reaction ",reac.name, "missing substrate and product"
+ else:
+ kfl = reaction.createKineticLaw()
+ if reacSub:
+ noofSub,sRateLaw = getSubprd(cremodel_,False,"sub",reacSub)
+ if noofSub:
+ cleanReacname = cleanReacname+"_"+str(reac.getId().value)+"_"+str(reac.getDataIndex())+"_"
+ kfparm = idBeginWith(cleanReacname)+"_"+"Kf"
+ sRL = idBeginWith(cleanReacname) + "_Kf * " + sRateLaw
+ unit = parmUnit( noofSub-1 ,cremodel_)
+ printParameters( kfl,kfparm,Kf,unit );
+ kl_s = sRL
+ else:
+ print reac.name + " has no substrate"
+ return -2
+ else:
+ print " Substrate missing for reaction ",reac.name
+
+ if reacPrd:
+ noofPrd,pRateLaw = getSubprd(cremodel_,False,"prd",reacPrd)
+ if noofPrd:
+ if Kb:
+ kbparm = idBeginWith(cleanReacname)+"_"+"Kb"
+ pRL = idBeginWith(cleanReacname) + "_Kb * " + pRateLaw
+ unit = parmUnit( noofPrd-1 , cremodel_)
+ printParameters( kfl,kbparm,Kb,unit );
+ kl_s = kl_s+ "- "+pRL
+ else:
+ print reac.name + " has no product"
+ return -2
+ else:
+ print " Product missing for reaction ",reac.name
+ kfl.setFormula(kl_s)
+
+def writeFunc(modelpath,cremodel_):
+ funcs = wildcardFind(modelpath+'/##[ISA=Function]')
+ #if func:
+ for func in funcs:
+ if func:
+ fName = idBeginWith( convertSpecialChar(func.parent.name+"_"+str(func.parent.getId().value)+"_"+str(func.parent.getDataIndex())+"_"))
+ item = func.path+'/x[0]'
+ sumtot = moose.element(item).neighbors["input"]
+ expr = moose.element(func).expr
+ for i in range(0,len(sumtot)):
+ v ="x"+str(i)
+ if v in expr:
+ z = str(convertSpecialChar(sumtot[i].name+"_"+str(moose.element(sumtot[i]).getId().value)+"_"+str(moose.element(sumtot[i]).getDataIndex()))+"_")
+ expr = expr.replace(v,z)
+ rule = cremodel_.createAssignmentRule()
+ rule.setVariable( fName )
+ rule.setFormula( expr )
+
+def convertNotesSpecialChar(str1):
+ d = {"&":"_and","<":"_lessthan_",">":"_greaterthan_","BEL":"°"}
+ for i,j in d.iteritems():
+ str1 = str1.replace(i,j)
+ #stripping \t \n \r and space from begining and end of string
+ str1 = str1.strip(' \t\n\r')
+ return str1
+def getGroupinfo(element):
+ # Note: At this time I am assuming that if group exist (incase of Genesis)
+ # 1. for 'pool' its between compartment and pool, /modelpath/Compartment/Group/pool
+ # 2. for 'enzComplx' in case of ExpilcityEnz its would be, /modelpath/Compartment/Group/Pool/Enz/Pool_cplx
+ # For these cases I have checked, but subgroup may exist then this bit of code need to cleanup further down
+ # if /modelpath/Compartment/Group/Group1/Pool, then I check and get Group1
+ # And /modelpath is also a NeutralObject,I stop till I find Compartment
+
+ while not mooseIsInstance(element, ["Neutral"]) and not mooseIsInstance(element,["CubeMesh","CyclMesh"]):
+ element = element.parent
+ return element
+
+def mooseIsInstance(element, classNames):
+ return moose.element(element).__class__.__name__ in classNames
+
+def findCompartment(element):
+ while not mooseIsInstance(element,["CubeMesh","CyclMesh"]):
+ element = element.parent
+ return element
+
+def idBeginWith( name ):
+ changedName = name;
+ if name[0].isdigit() :
+ changedName = "_"+name
+ return changedName;
+
+def convertSpecialChar(str1):
+ d = {"&":"_and","<":"_lessthan_",">":"_greaterthan_","BEL":"°","-":"_minus_","'":"_prime_",
+ "+": "_plus_","*":"_star_","/":"_slash_","(":"_bo_",")":"_bc_",
+ "[":"_sbo_","]":"_sbc_",".":"_dot_"," ":"_"
+ }
+ for i,j in d.iteritems():
+ str1 = str1.replace(i,j)
+ return str1
+
+def writeSpecies(modelpath,cremodel_,sbmlDoc):
+ #getting all the species
+ for spe in wildcardFind(modelpath+'/##[ISA=PoolBase]'):
+ sName = convertSpecialChar(spe.name)
+ comptVec = findCompartment(spe)
+ speciannoexist = False;
+ speciGpname = ""
+
+ if not isinstance(moose.element(comptVec),moose.ChemCompt):
+ return -2
+ else:
+ compt = comptVec.name+"_"+str(comptVec.getId().value)+"_"+str(comptVec.getDataIndex())+"_"
+ s1 = cremodel_.createSpecies()
+ spename = sName+"_"+str(spe.getId().value)+"_"+str(spe.getDataIndex())+"_"
+ spename = str(idBeginWith(spename))
+ s1.setId(spename)
+
+ if spename.find("cplx") != -1 and isinstance(moose.element(spe.parent),moose.EnzBase):
+ enz = spe.parent
+ if (moose.element(enz.parent),moose.PoolBase):
+ #print " found a cplx name ",spe.parent, moose.element(spe.parent).parent
+ enzname = enz.name
+ enzPool = (enz.parent).name
+ sName = convertSpecialChar(enzPool+"_"+enzname+"_"+sName)
+
+
+ s1.setName(sName)
+ s1.setInitialAmount(spe.nInit)
+ s1.setCompartment(compt)
+ # Setting BoundaryCondition and constant as per this rule for BufPool
+ # -constanst -boundaryCondition -has assignment/rate Rule -can be part of sub/prd
+ # false true yes yes
+ # true true no yes
+ if spe.className == "BufPool" or spe.className == "ZombieBufPool" :
+ #BoundaryCondition is made for buff pool
+ s1.setBoundaryCondition(True);
+
+ if moose.exists(spe.path+'/func'):
+ bpf = moose.element(spe.path)
+ for fp in bpf.children:
+ if fp.className =="Function" or fp.className == "ZombieFunction":
+ if len(moose.element(fp.path+'/x').neighbors["input"]) > 0:
+ s1.setConstant(False)
+ else:
+ #if function exist but sumtotal object doesn't exist
+ spe_constTrue.append(spename)
+ s1.setConstant(True)
+ else:
+ spe_constTrue.append(spename)
+ s1.setConstant(True)
+ else:
+ #if not bufpool then Pool, then
+ s1.setBoundaryCondition(False)
+ s1.setConstant(False)
+ s1.setUnits("substance")
+ s1.setHasOnlySubstanceUnits( True )
+ if moose.exists(spe.path+'/info'):
+ Anno = moose.Annotator(spe.path+'/info')
+ notesS = Anno.notes
+ if notesS != "":
+ cleanNotesS= convertNotesSpecialChar(notesS)
+ notesStringS = "<body xmlns=\"http://www.w3.org/1999/xhtml\">\n \t \t"+ cleanNotesS + "\n\t </body>"
+ s1.setNotes(notesStringS)
+ #FindGroupName
+ element = moose.element(spe)
+ ele = getGroupinfo(element)
+ if ele.className == "Neutral":
+ speciGpname = "<moose:Group>"+ ele.name + "</moose:Group>\n"
+ speciannoexist = True
+ if speciannoexist :
+ speciAnno = "<moose:ModelAnnotation>\n"
+ if speciGpname:
+ speciAnno = speciAnno + speciGpname
+ speciAnno = speciAnno+ "</moose:ModelAnnotation>"
+ return True
+
+def writeCompt(modelpath,cremodel_):
+ #getting all the compartments
+ for compt in wildcardFind(modelpath+'/##[ISA=ChemCompt]'):
+ comptName = convertSpecialChar(compt.name)
+ #converting m3 to litre
+ size =compt.volume*pow(10,3)
+ ndim = compt.numDimensions
+ c1 = cremodel_.createCompartment()
+ c1.setId(str(idBeginWith(comptName+"_"+str(compt.getId().value)+"_"+str(compt.getDataIndex())+"_")))
+ c1.setName(comptName)
+ c1.setConstant(True)
+ c1.setSize(size)
+ c1.setSpatialDimensions(ndim)
+ c1.setUnits('volume')
+
+#write Simulation runtime,simdt,plotdt
+def writeSimulationAnnotation(modelpath):
+ modelAnno = ""
+ if moose.exists(modelpath+'/info'):
+ mooseclock = moose.Clock('/clock')
+ modelAnno ="<moose:ModelAnnotation>\n"
+ modelAnnotation = moose.element(modelpath+'/info')
+ modelAnno = modelAnno+"<moose:ModelTime> "+str(modelAnnotation.runtime)+" </moose:ModelTime>\n"
+ modelAnno = modelAnno+"<moose:ModelSolver> "+modelAnnotation.solver+" </moose:ModelSolver>\n"
+ modelAnno = modelAnno+"<moose:simdt>"+ str(mooseclock.dts[11]) + " </moose:simdt>\n";
+ modelAnno = modelAnno+"<moose:plotdt> " + str(mooseclock.dts[18]) +" </moose:plotdt>\n";
+ plots = "";
+ graphs = moose.wildcardFind(modelpath+"/##[TYPE=Table2]")
+ for gphs in range(0,len(graphs)):
+ gpath = graphs[gphs].neighbors['requestOut']
+ if len(gpath) != 0:
+ q = moose.element(gpath[0])
+ ori = q.path
+ graphSpefound = False
+ while not(isinstance(moose.element(q),moose.CubeMesh)):
+ q = q.parent
+ graphSpefound = True
+ if graphSpefound:
+ if not plots:
+ plots = ori[ori.find(q.name)-1:len(ori)]
+ else:
+ plots = plots + "; "+ori[ori.find(q.name)-1:len(ori)]
+ if plots != " ":
+ modelAnno = modelAnno+ "<moose:plots> "+ plots+ "</moose:plots>\n";
+ modelAnno = modelAnno+"</moose:ModelAnnotation>"
+ return modelAnno
+
+def writeUnits(cremodel_):
+ unitVol = cremodel_.createUnitDefinition()
+ unitVol.setId( "volume")
+ unit = unitVol.createUnit()
+ unit.setKind(UNIT_KIND_LITRE)
+ unit.setMultiplier(1.0)
+ unit.setExponent(1.0)
+ unit.setScale(0)
+
+ unitSub = cremodel_.createUnitDefinition()
+ unitSub.setId("substance")
+ unit = unitSub.createUnit()
+ unit.setKind( UNIT_KIND_ITEM )
+ unit.setMultiplier(1)
+ unit.setExponent(1.0)
+ unit.setScale(0)
+
+
+def validateModel( sbmlDoc ):
+ #print " sbmlDoc ",sbmlDoc.toSBML()
+ if ( not sbmlDoc ):
+ print "validateModel: given a null SBML Document"
+ return False
+ consistencyMessages = ""
+ validationMessages = ""
+ noProblems = True
+ numCheckFailures = 0
+ numConsistencyErrors = 0
+ numConsistencyWarnings = 0
+ numValidationErrors = 0
+ numValidationWarnings = 0
+ #Once the whole model is done and before it gets written out,
+ #it's important to check that the whole model is in fact complete, consistent and valid.
+ numCheckFailures = sbmlDoc.checkInternalConsistency()
+ if ( numCheckFailures > 0 ):
+ noProblems = False
+ for i in range(0,numCheckFailures ):
+ sbmlErr = sbmlDoc.getError(i);
+ if ( sbmlErr.isFatal() or sbmlErr.isError() ):
+ ++numConsistencyErrors;
+ else:
+ ++numConsistencyWarnings
+ constStr = sbmlDoc.printErrors()
+ consistencyMessages = constStr
+
+ #If the internal checks fail, it makes little sense to attempt
+ #further validation, because the model may be too compromised to
+ #be properly interpreted.
+ if ( numConsistencyErrors > 0 ):
+ consistencyMessages += "Further validation aborted.";
+ else:
+ numCheckFailures = sbmlDoc.checkConsistency()
+ #numCheckFailures = sbmlDoc.checkL3v1Compatibility()
+ if ( numCheckFailures > 0 ):
+ noProblems = False;
+ for i in range(0, (numCheckFailures ) ):
+ consistencyMessages = sbmlDoc.getErrorLog().toString()
+ sbmlErr = sbmlDoc.getError(i);
+ if ( sbmlErr.isFatal() or sbmlErr.isError() ):
+ ++numValidationErrors;
+ else:
+ ++numValidationWarnings;
+ warning = sbmlDoc.getErrorLog().toString()
+ oss = sbmlDoc.printErrors()
+ validationMessages = oss
+ if ( noProblems ):
+ return True
+ else:
+ if consistencyMessages != "":
+ print " consistency Warning: "+consistencyMessages
+
+ if ( numConsistencyErrors > 0 ):
+ if numConsistencyErrors == 1: t = ""
+ else: t="s"
+ print "ERROR: encountered " + numConsistencyErrors + " consistency error" +t+ " in model '" + sbmlDoc.getModel().getId() + "'."
+ if ( numConsistencyWarnings > 0 ):
+ if numConsistencyWarnings == 1:
+ t1 = ""
+ else: t1 ="s"
+ print "Notice: encountered " + numConsistencyWarnings +" consistency warning" + t + " in model '" + sbmlDoc.getModel().getId() + "'."
+
+ if ( numValidationErrors > 0 ):
+ if numValidationErrors == 1:
+ t2 = ""
+ else: t2 ="s"
+ print "ERROR: encountered " + numValidationErrors + " validation error" + t2 + " in model '" + sbmlDoc.getModel().getId() + "'."
+ if ( numValidationWarnings > 0 ):
+ if numValidationWarnings == 1:
+ t3 = ""
+ else: t3 = "s"
+
+ print "Notice: encountered " + numValidationWarnings + " validation warning" + t3 + " in model '" + sbmlDoc.getModel().getId() + "'."
+
+ print validationMessages;
+ return ( numConsistencyErrors == 0 and numValidationErrors == 0)
+ #return ( numConsistencyErrors == 0 and numValidationErrors == 0, consistencyMessages)
+
+if __name__ == "__main__":
+
+ filepath = sys.argv[1]
+ path = sys.argv[2]
+
+ f = open(filepath, 'r')
+
+ if path == '':
+ loadpath = filepath[filepath.rfind('/'):filepath.find('.')]
+ else:
+ loadpath = path
+
+ moose.loadModel(filepath,loadpath,"gsl")
+
+ written = mooseWriteSBML(loadpath,filepath)
+ if written:
+ print " File written to ",written
+ else:
+ print " could not write model to SBML file"
+
\ No newline at end of file
diff --git a/moose-core/python/moose/genesis/_main.py b/moose-core/python/moose/genesis/_main.py
index f66d900047ed9fb2c80adbfe8dcd5e9973b657b4..67a15b98a9308c8b95e5cfd44d21c06606322d4f 100644
--- a/moose-core/python/moose/genesis/_main.py
+++ b/moose-core/python/moose/genesis/_main.py
@@ -68,7 +68,6 @@ def write( modelpath, filename,sceneitems=None):
#This is when it comes from Gui where the objects are already layout on to scene
# so using thoes co-ordinates
xmin,ymin,xmax,ymax,positionInfoExist = getCor(modelpath,sceneitems)
-
gtId_vol = writeCompartment(modelpath,compt,f)
writePool(modelpath,f,gtId_vol)
reacList = writeReac(modelpath,f)
@@ -300,7 +299,7 @@ def storePlotMsgs( tgraphs,f):
bg = getColorCheck(bg,GENESIS_COLOR_SEQUENCE)
tabPath = re.sub("\[[0-9]+\]", "", tabPath)
s = s+"addmsg /kinetics/" + trimPath( poolEle ) + " " + tabPath + \
- " PLOT Co *" + poolName + " *" + bg +"\n";
+ " PLOT Co *" + poolName + " *" + str(bg) +"\n";
f.write(s)
def writeplot( tgraphs,f ):
@@ -340,36 +339,36 @@ def writePool(modelpath,f,volIndex):
else:
slave_enable = 0
break
-
- xp = cord[p]['x']
- yp = cord[p]['y']
- x = ((xp-xmin)/(xmax-xmin))*multi
- y = ((yp-ymin)/(ymax-ymin))*multi
- #y = ((ymax-yp)/(ymax-ymin))*multi
-
- pinfo = p.path+'/info'
- if exists(pinfo):
- color = Annotator(pinfo).getField('color')
- color = getColorCheck(color,GENESIS_COLOR_SEQUENCE)
-
- textcolor = Annotator(pinfo).getField('textColor')
- textcolor = getColorCheck(textcolor,GENESIS_COLOR_SEQUENCE)
- geometryName = volIndex[p.volume]
- volume = p.volume * NA * 1e-3
-
- f.write("simundump kpool /kinetics/" + trimPath(p) + " 0 " +
- str(p.diffConst) + " " +
- str(0) + " " +
- str(0) + " " +
- str(0) + " " +
- str(p.nInit) + " " +
- str(0) + " " + str(0) + " " +
- str(volume)+ " " +
- str(slave_enable) +
- " /kinetics"+ geometryName + " " +
- str(color) +" " + str(textcolor) + " " + str(int(x)) + " " + str(int(y)) + " "+ str(0)+"\n")
+ #Eliminated enzyme complex pool
+ if ((p.parent).className != "Enz" and (p.parent).className != "ZombieEnz"):
+ xp = cord[p]['x']
+ yp = cord[p]['y']
+ x = ((xp-xmin)/(xmax-xmin))*multi
+ y = ((yp-ymin)/(ymax-ymin))*multi
+ #y = ((ymax-yp)/(ymax-ymin))*multi
+ pinfo = p.path+'/info'
+ if exists(pinfo):
+ color = Annotator(pinfo).getField('color')
+ color = getColorCheck(color,GENESIS_COLOR_SEQUENCE)
+
+ textcolor = Annotator(pinfo).getField('textColor')
+ textcolor = getColorCheck(textcolor,GENESIS_COLOR_SEQUENCE)
+ geometryName = volIndex[p.volume]
+ volume = p.volume * NA * 1e-3
+ f.write("simundump kpool /kinetics/" + trimPath(p) + " 0 " +
+ str(p.diffConst) + " " +
+ str(0) + " " +
+ str(0) + " " +
+ str(0) + " " +
+ str(p.nInit) + " " +
+ str(0) + " " + str(0) + " " +
+ str(volume)+ " " +
+ str(slave_enable) +
+ " /kinetics"+ geometryName + " " +
+ str(color) +" " + str(textcolor) + " " + str(int(x)) + " " + str(int(y)) + " "+ str(0)+"\n")
# print " notes ",notes
# return notes
+
def getColorCheck(color,GENESIS_COLOR_SEQUENCE):
if isinstance(color, str):
if color.startswith("#"):
@@ -407,6 +406,9 @@ def getxyCord(xcord,ycord,list1,sceneitems):
co = sceneitems[item]
xpos = co.scenePos().x()
ypos =-co.scenePos().y()
+ #xpos = co['x']
+ #ypos = co['y']
+
cord[item] ={ 'x': xpos,'y':ypos}
xcord.append(xpos)
ycord.append(ypos)
@@ -420,7 +422,8 @@ def getCor(modelRoot,sceneitems):
xmin = ymin = 0.0
xmax = ymax = 1.0
positionInfoExist = False
- xcord = ycord = []
+ xcord = []
+ ycord = []
mollist = realist = enzlist = cplxlist = tablist = funclist = []
meshEntryWildcard = '/##[ISA=ChemCompt]'
if modelRoot != '/':
@@ -439,18 +442,25 @@ def getCor(modelRoot,sceneitems):
elif isinstance(element(m),PoolBase):
mollist.append(m)
objInfo =m.path+'/info'
-
+ #xx = xyPosition(objInfo,'x')
+ #yy = xyPosition(objInfo,'y')
+
+
if sceneitems == None:
xx = xyPosition(objInfo,'x')
yy = xyPosition(objInfo,'y')
else:
- c = sceneitems[m]
- xx = c.scenePos().x()
- yy =-c.scenePos().y()
-
+ c = sceneitems[m]
+ xx = c.scenePos().x()
+ yy =-c.scenePos().y()
+ #listq = sceneitems[m]
+ #xx = listq['x']
+ #yy = listq['y']
+
cord[m] ={ 'x': xx,'y':yy}
xcord.append(xx)
ycord.append(yy)
+
getxyCord(xcord,ycord,realist,sceneitems)
getxyCord(xcord,ycord,enzlist,sceneitems)
getxyCord(xcord,ycord,funclist,sceneitems)
@@ -582,12 +592,20 @@ def writeGui( f ):
"simundump xtext /file/notes 0 1\n")
def writeNotes(modelpath,f):
notes = ""
- items = wildcardFind(modelpath+"/##[ISA=ChemCompt],/##[ISA=ReacBase],/##[ISA=PoolBase],/##[ISA=EnzBase],/##[ISA=Function],/##[ISA=StimulusTable]")
+ items = []
+ items = wildcardFind(modelpath+"/##[ISA=ChemCompt]") +\
+ wildcardFind(modelpath+"/##[ISA=PoolBase]") +\
+ wildcardFind(modelpath+"/##[ISA=ReacBase]") +\
+ wildcardFind(modelpath+"/##[ISA=EnzBase]") +\
+ wildcardFind(modelpath+"/##[ISA=Function]") +\
+ wildcardFind(modelpath+"/##[ISA=StimulusTable]")
for item in items:
- info = item.path+'/info'
- notes = Annotator(info).getField('notes')
- if (notes):
- f.write("call /kinetics/"+ trimPath(item)+"/notes LOAD \ \n\""+Annotator(info).getField('notes')+"\"\n")
+ if exists(item.path+'/info'):
+ info = item.path+'/info'
+ notes = Annotator(info).getField('notes')
+ if (notes):
+ f.write("call /kinetics/"+ trimPath(item)+"/notes LOAD \ \n\""+Annotator(info).getField('notes')+"\"\n")
+
def writeFooter1(f):
f.write("\nenddump\n // End of dump\n")
def writeFooter2(f):
diff --git a/moose-core/python/moose/merge.py b/moose-core/python/moose/merge.py
new file mode 100644
index 0000000000000000000000000000000000000000..aaf05c12b915d6cc967dac331530fdc92ebd0042
--- /dev/null
+++ b/moose-core/python/moose/merge.py
@@ -0,0 +1,247 @@
+
+#*******************************************************************
+# * File: merge.py
+# * Description:
+# * Author: HarshaRani
+# * E-mail: hrani@ncbs.res.in
+# ********************************************************************/
+# **********************************************************************
+#** This program is part of 'MOOSE', the
+#** Messaging Object Oriented Simulation Environment,
+#** also known as GENESIS 3 base code.
+#** copyright (C) 2003-2016 Upinder S. Bhalla. and NCBS
+#Created : Friday June 13 12:19:00 2016(+0530)
+#Version
+#Last-Updated:Tuesday June 21 17.48.37
+# By: Harsha
+#**********************************************************************/
+
+# This program is used to merge models
+# -- Model B is merged to A
+# -- Rules are
+# ## check for compartment in B exist in A
+# *** If compartment from model B doesn't exist in model A, then copy entire compartment from B to A
+# *** If compartment from model B exist in model A
+# ^^^^ check the volume of compartment of B as compared to A
+# !!!!! If same, then copy all the moose object which doesn't exist in A and reference to both mooseId
+# which is used for connecting objects.
+#
+# ^^^^ If volume of compartment of model B is different then change the volume of compartment of model B same as A
+# !!!! If same, then copy all the moose object which doesn't exist in A and reference to both mooseId
+# which is used for connecting objects
+
+# &&&&&& copying pools from compartment from B to A is easy
+# &&&&& but while copying reaction and enzyme check if the same reaction exist
+# -- if same reaction name exists
+# -- Yes
+# 1) check if substrate and product are same as compartment from model B to compartment modelA
+# --yes do nothing
+# --No then duplicate the reaction in model A and connect the message of approraite sub/prd
+# and warn the user the same reaction name with different sub or product
+# -- No
+# copy the reaction
+
+import sys
+from . import _moose as moose
+
+def merge(A,B):
+ #load models into moose and solver's are deleted
+ apath = loadModels(A)
+ bpath = loadModels(B)
+
+ comptAdict = comptList(apath)
+ comptBdict = comptList(bpath)
+
+ for key in comptBdict.keys():
+
+ if not comptAdict.has_key(key):
+ # comptBdict[key] - compartment from model B which does not exist in model A
+ moose.copy(comptBdict[key],moose.element(apath))
+ else:
+ war_msg = ""
+ copied , duplicated = [],[]
+
+ if not (comptAdict[key].volume == comptBdict[key].volume):
+ #change volume of ModelB same as ModelA
+ volumeA = comptAdict[key].volume
+ comptBdict[key].volume = volumeA
+
+ #Merging Pool
+ poolName_a = []
+ poolListina = moose.wildcardFind(comptAdict[key].path+'/##[ISA=PoolBase]')
+ if poolListina:
+ neutral_compartment = findgroup_compartment(poolListina[0])
+ for pl in poolListina:
+ poolName_a.append(pl.name)
+
+ for pool in moose.wildcardFind(comptBdict[key].path+'/##[ISA=PoolBase]'):
+ if not pool.name in poolName_a :
+ #pool has compartment(assume its direct pool ),so copy under kinetics
+ if ((pool.parent).className == "CubeMesh" or (pool.parent).className == "Neutral"):
+ c = moose.copy(pool,neutral_compartment)
+ copied.append(c)
+ elif (pool.parent).className == "ZombieEnz" or (pool.parent).className == "Enz":
+ print " Pool not in modelA but enz parent",pool.name
+ pass
+ else:
+ print " Check this pool, parent which doesn't have ChemCompt or Enz",
+
+ #Mergering StimulusTable
+ stimName_a = []
+ stimListina = moose.wildcardFind(comptAdict[key].path+'/##[ISA=StimulusTable]')
+ if stimListina:
+ neutral_compartment = findgroup_compartment(stimListina[0])
+ for st in stimListina:
+ stimName_a.append(st.name)
+ for stb in moose.wildcardFind(comptBdict[key].path+'/##[ISA=StimulusTable]'):
+ if stb.name in stimName_a:
+ sA = comptAdict[key].path+'/'+stb.name
+ sB = comptBdict[key].path+'/'+stb.name
+ stAOutput = subprdList(sA,"output")
+ stBOutput = subprdList(sB,"output")
+ sas = set(stAOutput)
+ sbs = set(stBOutput)
+ uniq = (sas.union(sbs) - sas.intersection(sbs))
+ for u in uniq:
+ if u not in stAOutput:
+ src = moose.element(sA)
+ des = moose.element(comptAdict[key].path+'/'+u)
+ moose.connect(src,'output',des,'setConcInit')
+ else:
+ st1 = moose.StimulusTable(comptAdict[key].path+'/'+stb.name)
+ for sb in sbs:
+ des = moose.element(comptAdict[key].path+'/'+sb)
+ moose.connect(st1,'output',des,'setConcInit')
+ #Mergering Reaction
+ reacName_a = []
+ reacListina = moose.wildcardFind(comptAdict[key].path+'/##[ISA=ReacBase]')
+ if reacListina:
+ neutral_compartment = findgroup_compartment(poolListina[0])
+
+ for re in reacListina:
+ reacName_a.append(re.name)
+ for reac in moose.wildcardFind(comptBdict[key].path+'/##[ISA=ReacBase]'):
+ if reac.name in reacName_a:
+
+ rA = comptAdict[key].path+'/'+reac.name
+ rB = comptBdict[key].path+'/'+reac.name
+
+ rAsubname,rBsubname,rAprdname,rBprdname = [], [], [], []
+ rAsubname = subprdList(rA,"sub")
+ rBsubname = subprdList(rB,"sub")
+ rAprdname = subprdList(rA,"prd")
+ rBprdname = subprdList(rB,"prd")
+
+ aS = set(rAsubname)
+ bS = set(rBsubname)
+ aP = set(rAprdname)
+ bP = set(rBprdname)
+
+ hasSameSub,hasSamePrd = True,True
+ hassameSlen,hassamePlen = False,False
+
+ hasSameSub = not (len (aS.union(bS) - aS.intersection(bS)))
+ hasSamePrd = not (len(aP.union(bP) - aP.intersection(bP)))
+
+ hassameSlen = ( len(rAsubname) == len(rBsubname))
+ hassamePlen = ( len(rAprdname) == len(rBprdname))
+
+
+ if not all((hasSameSub,hasSamePrd,hassameSlen,hassamePlen)):
+ war_msg = war_msg +"Reaction \""+reac.name+ "\" also contains in modelA but with different"
+ if not all((hasSameSub,hassameSlen)):
+ war_msg = war_msg+ " substrate "
+
+ if not all((hasSamePrd, hassamePlen)):
+ war_msg = war_msg+ " product"
+ war_msg = war_msg +", reaction is duplicated in modelA. \nModeler should decide to keep or remove this reaction"
+
+ reac = moose.Reac(comptAdict[key].path+'/'+reac.name+"_duplicated")
+ mooseConnect(comptAdict[key].path,reac,rBsubname,"sub")
+ mooseConnect(comptAdict[key].path,reac,rBprdname,"prd")
+
+ duplicated.append(reac)
+
+ elif not reac.name in reacName_a :
+ #reac has compartment(assume its direct reac ),so copy under kinetics
+ if ((reac.parent).className == "CubeMesh" or (reac.parent).className == "Neutral"):
+ c = moose.copy(reac,neutral_compartment)
+ copied.append(c)
+
+ rBsubname, rBprdname = [],[]
+ rBsubname = subprdList(reac,"sub")
+ rBprdname = subprdList(reac,"prd")
+ mooseConnect(comptAdict[key].path,reac,rBsubname,"sub")
+ mooseConnect(comptAdict[key].path,reac,rBprdname,"prd")
+ print "\ncopied: ", copied, \
+ "\n\nDuplicated: ",duplicated, \
+ "\n\nwarning: ",war_msg
+ return copied,duplicated,war_msg
+def loadModels(filename):
+ apath = '/'
+
+ apath = filename[filename.rfind('/'): filename.rfind('.')]
+
+ moose.loadModel(filename,apath)
+
+ #Solvers are removed
+ deleteSolver(apath)
+ return apath
+
+def comptList(modelpath):
+ comptdict = {}
+ for ca in moose.wildcardFind(modelpath+'/##[ISA=ChemCompt]'):
+ comptdict[ca.name] = ca
+ return comptdict
+
+def mooseConnect(modelpath,reac,spList,sptype):
+ for spl in spList:
+ spl_id = moose.element(modelpath+'/'+spl)
+ reac_id = moose.element(modelpath+'/'+reac.name)
+ if sptype == "sub":
+ m = moose.connect( reac_id, "sub", spl_id, 'reac' )
+ else:
+ moose.connect( reac_id, "prd", spl_id, 'reac' )
+
+def deleteSolver(modelRoot):
+ compts = moose.wildcardFind(modelRoot+'/##[ISA=ChemCompt]')
+ for compt in compts:
+ if moose.exists(compt.path+'/stoich'):
+ st = moose.element(compt.path+'/stoich')
+ st_ksolve = st.ksolve
+ moose.delete(st)
+ if moose.exists((st_ksolve).path):
+ moose.delete(st_ksolve)
+
+def subprdList(reac,subprd):
+ rtype = moose.element(reac).neighbors[subprd]
+ rname = []
+ for rs in rtype:
+ rname.append(rs.name)
+ return rname
+
+def findCompartment(element):
+ while not mooseIsInstance(element,["CubeMesh","CyclMesh"]):
+ element = element.parent
+ return element
+def mooseIsInstance(element, classNames):
+ #print classNames
+ #print moose.element(element).__class__.__name__ in classNames
+ return moose.element(element).__class__.__name__ in classNames
+
+def findgroup_compartment(element):
+ #Try finding Group which is Neutral but it should exist before Compartment, if Compartment exist then stop at Comparment
+ while not mooseIsInstance(element,"Neutral"):
+ if mooseIsInstance(element,["CubeMesh","CyclMesh"]):
+ return element
+ element = element.parent
+ return element
+if __name__ == "__main__":
+
+ model1 = '/home/harsha/genesis_files/gfile/acc12.g'
+ model2 = '/home/harsha/Trash/acc12_withadditionPool.g'
+ #model1 = '/home/harsha/Trash/modelA.g'
+ #model2 = '/home/harsha/Trash/modelB.g'
+ model1 = '/home/harsha/genesis_files/gfile/acc44.g'
+ model2 = '/home/harsha/genesis_files/gfile/acc45.g'
+ mergered = merge(model1,model2)
\ No newline at end of file
diff --git a/moose-core/python/rdesigneur/rdesigneur.py b/moose-core/python/rdesigneur/rdesigneur.py
index cb46f26b51fbdfb949044fe5dbf52986c279e064..803d3144b5cb6f324daefb2c018e7afe6a8334c7 100644
--- a/moose-core/python/rdesigneur/rdesigneur.py
+++ b/moose-core/python/rdesigneur/rdesigneur.py
@@ -1,5 +1,5 @@
#########################################################################
-## rdesigneur0_4.py ---
+## rdesigneur0_5.py ---
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
@@ -27,6 +27,10 @@ import rmoogli
from rdesigneurProtos import *
from moose.neuroml.NeuroML import NeuroML
from moose.neuroml.ChannelML import ChannelML
+import lxml
+from lxml import etree
+import h5py as h5
+import csv
#EREST_ACT = -70e-3
@@ -76,7 +80,8 @@ class rdesigneur:
adaptorList= [],
stimList = [],
plotList = [],
- moogList = []
+ moogList = [],
+ params = None
):
""" Constructor of the rdesigner. This just sets up internal fields
for the model building, it doesn't actually create any objects.
@@ -108,14 +113,20 @@ class rdesigneur:
self.chanDistrib = chanDistrib
self.chemDistrib = chemDistrib
+ self.params = params
+
self.adaptorList = adaptorList
self.stimList = stimList
self.plotList = plotList
+ self.saveList = plotList #ADDED BY Sarthak
+ self.saveAs = []
self.moogList = moogList
self.plotNames = []
+ self.saveNames = []
self.moogNames = []
self.cellPortionElist = []
self.spineComptElist = []
+ self.tabForXML = []
if not moose.exists( '/library' ):
library = moose.Neutral( '/library' )
@@ -172,6 +183,7 @@ class rdesigneur:
self._buildStims()
self._configureClocks()
self._printModelStats()
+ self._savePlots()
except BuildError as msg:
print("Error: rdesigneur: model build failed:", msg)
@@ -485,6 +497,7 @@ class rdesigneur:
kf = knownFields[field] # Find the field to decide type.
if ( kf[0] == 'CaConcBase' or kf[0] == 'ChanBase' ):
objList = self._collapseElistToPathAndClass( comptList, plotSpec[2], kf[0] )
+ # print ("objList: ", len(objList), kf[1])
return objList, kf[1]
elif (field == 'n' or field == 'conc' ):
path = plotSpec[2]
@@ -538,8 +551,6 @@ class rdesigneur:
pair = i[0] + " " + i[1]
dendCompts = self.elecid.compartmentsFromExpression[ pair ]
spineCompts = self.elecid.spinesFromExpression[ pair ]
- #print( "DENDENDENDNEDN = ", len(dendCompts), pair )
- #print( "SPINESPINESPINE = ", len(spineCompts), pair )
plotObj, plotField = self._parseComptField( dendCompts, i, knownFields )
plotObj2, plotField2 = self._parseComptField( spineCompts, i, knownFields )
assert( plotField == plotField2 )
@@ -613,7 +624,212 @@ class rdesigneur:
pylab.plot( t, j.vector * i[3] )
if len( self.moogList ) > 0:
pylab.ion()
- pylab.show()
+ pylab.show(block=True)
+ self._save() #This calls the _save function which saves only if the filenames have been specified
+
+ ################################################################
+ # Here we get the time-series data and write to various formats
+ ################################################################
+ #[TO DO] Add NSDF output function
+ '''
+ The author of the functions -- [_savePlots(), _getTimeSeriesTable(), _writeXML(), _writeCSV(), _saveFormats(), _save()] is
+ Sarthak Sharma.
+ Email address: sarthaks442@gmail.com
+ '''
+
+ def _savePlots( self ):
+
+ knownFields = {
+ 'Vm':('CompartmentBase', 'getVm', 1000, 'Memb. Potential (mV)' ),
+ 'Im':('CompartmentBase', 'getIm', 1e9, 'Memb. current (nA)' ),
+ 'inject':('CompartmentBase', 'getInject', 1e9, 'inject current (nA)' ),
+ 'Gbar':('ChanBase', 'getGbar', 1e9, 'chan max conductance (nS)' ),
+ 'Gk':('ChanBase', 'getGk', 1e9, 'chan conductance (nS)' ),
+ 'Ik':('ChanBase', 'getIk', 1e9, 'chan current (nA)' ),
+ 'Ca':('CaConcBase', 'getCa', 1e3, 'Ca conc (uM)' ),
+ 'n':('PoolBase', 'getN', 1, '# of molecules'),
+ 'conc':('PoolBase', 'getConc', 1000, 'Concentration (uM)' )
+ }
+
+ save_graphs = moose.Neutral( self.modelPath + '/save_graphs' )
+ dummy = moose.element( '/' )
+ k = 0
+
+ for i in self.saveList:
+ pair = i[0] + " " + i[1]
+ dendCompts = self.elecid.compartmentsFromExpression[ pair ]
+ spineCompts = self.elecid.spinesFromExpression[ pair ]
+ plotObj, plotField = self._parseComptField( dendCompts, i, knownFields )
+ plotObj2, plotField2 = self._parseComptField( spineCompts, i, knownFields )
+ assert( plotField == plotField2 )
+ plotObj3 = plotObj + plotObj2
+ numPlots = sum( i != dummy for i in plotObj3 )
+ if numPlots > 0:
+ save_tabname = save_graphs.path + '/save_plot' + str(k)
+ scale = knownFields[i[3]][2]
+ units = knownFields[i[3]][3]
+ self.saveNames.append( ( save_tabname, i[4], k, scale, units ) )
+ k += 1
+ if i[3] == 'n' or i[3] == 'conc':
+ save_tabs = moose.Table2( save_tabname, numPlots )
+ else:
+ save_tabs = moose.Table( save_tabname, numPlots )
+ save_vtabs = moose.vec( save_tabs )
+ q = 0
+ for p in [ x for x in plotObj3 if x != dummy ]:
+ moose.connect( save_vtabs[q], 'requestOut', p, plotField )
+ q += 1
+
+ def _getTimeSeriesTable( self ):
+
+ '''
+ This function gets the list with all the details of the simulation
+ required for plotting.
+ This function adds flexibility in terms of the details
+ we wish to store.
+ '''
+
+ knownFields = {
+ 'Vm':('CompartmentBase', 'getVm', 1000, 'Memb. Potential (mV)' ),
+ 'Im':('CompartmentBase', 'getIm', 1e9, 'Memb. current (nA)' ),
+ 'inject':('CompartmentBase', 'getInject', 1e9, 'inject current (nA)' ),
+ 'Gbar':('ChanBase', 'getGbar', 1e9, 'chan max conductance (nS)' ),
+ 'Gk':('ChanBase', 'getGk', 1e9, 'chan conductance (nS)' ),
+ 'Ik':('ChanBase', 'getIk', 1e9, 'chan current (nA)' ),
+ 'Ca':('CaConcBase', 'getCa', 1e3, 'Ca conc (uM)' ),
+ 'n':('PoolBase', 'getN', 1, '# of molecules'),
+ 'conc':('PoolBase', 'getConc', 1000, 'Concentration (uM)' )
+ }
+
+ '''
+ This takes data from plotList
+ saveList is exactly like plotList but with a few additional arguments:
+ ->It will have a resolution option, i.e., the number of decimal figures to which the value should be rounded
+ ->There is a list of "saveAs" formats
+ With saveList, the user will able to set what all details he wishes to be saved.
+ '''
+
+ for i,ind in enumerate(self.saveNames):
+ pair = self.saveList[i][0] + " " + self.saveList[i][1]
+ dendCompts = self.elecid.compartmentsFromExpression[ pair ]
+ spineCompts = self.elecid.spinesFromExpression[ pair ]
+ # Here we get the object details from plotList
+ savePlotObj, plotField = self._parseComptField( dendCompts, self.saveList[i], knownFields )
+ savePlotObj2, plotField2 = self._parseComptField( spineCompts, self.saveList[i], knownFields )
+ savePlotObj3 = savePlotObj + savePlotObj2
+
+ rowList = list(ind)
+ save_vtab = moose.vec( ind[0] )
+ t = np.arange( 0, save_vtab[0].vector.size, 1 ) * save_vtab[0].dt
+
+ rowList.append(save_vtab[0].dt)
+ rowList.append(t)
+ rowList.append([jvec.vector * ind[3] for jvec in save_vtab]) #get values
+ rowList.append(self.saveList[i][3])
+ rowList.append(filter(lambda obj: obj.path != '/', savePlotObj3)) #this filters out dummy elements
+
+ if (type(self.saveList[i][-1])==int):
+ rowList.append(self.saveList[i][-1])
+ else:
+ rowList.append(12)
+
+ self.tabForXML.append(rowList)
+ rowList = []
+
+ timeSeriesTable = self.tabForXML # the list with all the details of plot
+ return timeSeriesTable
+
+ def _writeXML( self, filename, timeSeriesData ): #to write to XML file
+
+ plotData = timeSeriesData
+ print("[CAUTION] The '%s' file might be very large if all the compartments are to be saved." % filename)
+ root = etree.Element("TimeSeriesPlot")
+ parameters = etree.SubElement( root, "parameters" )
+ if self.params == None:
+ parameters.text = "None"
+ else:
+ assert(isinstance(self.params, dict)), "'params' should be a dictionary."
+ for pkey, pvalue in self.params.items():
+ parameter = etree.SubElement( parameters, str(pkey) )
+ parameter.text = str(pvalue)
+
+ #plotData contains all the details of a single plot
+ title = etree.SubElement( root, "timeSeries" )
+ title.set( 'title', str(plotData[1]))
+ title.set( 'field', str(plotData[8]))
+ title.set( 'scale', str(plotData[3]))
+ title.set( 'units', str(plotData[4]))
+ title.set( 'dt', str(plotData[5]))
+ p = []
+ assert(len(plotData[7]) == len(plotData[9]))
+
+ res = plotData[10]
+ for ind, jvec in enumerate(plotData[7]):
+ p.append( etree.SubElement( title, "data"))
+ p[-1].set( 'path', str(plotData[9][ind].path))
+ p[-1].text = ''.join( str(round(value,res)) + ' ' for value in jvec )
+
+ tree = etree.ElementTree(root)
+ tree.write(filename)
+
+ def _writeCSV(self, filename, timeSeriesData):
+
+ plotData = timeSeriesData
+ dataList = []
+ header = []
+ time = plotData[6]
+ res = plotData[10]
+
+ for ind, jvec in enumerate(plotData[7]):
+ header.append(plotData[9][ind].path)
+ dataList.append([round(value,res) for value in jvec.tolist()])
+ dl = [tuple(lst) for lst in dataList]
+ rows = zip(tuple(time), *dl)
+ header.insert(0, "time")
+
+ with open(filename, 'wb') as f:
+ writer = csv.writer(f, quoting=csv.QUOTE_MINIMAL)
+ writer.writerow(header)
+ for row in rows:
+ writer.writerow(row)
+
+ ##########****SAVING*****###############
+ def _saveFormats(self, timeSeriesData, k, *filenames):
+ "This takes in the filenames and writes to corresponding format."
+ if filenames:
+ for filename in filenames:
+ for name in filename:
+ print (name)
+ if name[-4:] == '.xml':
+ self._writeXML(name, timeSeriesData)
+ print(name, " written")
+ elif name[-4:] == '.csv':
+ self._writeCSV(name, timeSeriesData)
+ print(name, " written")
+ else:
+ print("not possible")
+ pass
+ else:
+ pass
+
+
+ def _save( self ):
+ timeSeriesTable = self._getTimeSeriesTable()
+ for i,sList in enumerate(self.saveList):
+
+ if (len(sList) >= 6) and (type(sList[5]) != int):
+ self.saveAs.extend(filter(lambda fmt: type(fmt)!=int, sList[5:]))
+ try:
+ timeSeriesData = timeSeriesTable[i]
+ except IndexError:
+ print("The object to be plotted has all dummy elements.")
+ pass
+ self._saveFormats(timeSeriesData, i, self.saveAs)
+ self.saveAs=[]
+ else:
+ pass
+ else:
+ pass
################################################################
# Here we set up the stims
@@ -1053,3 +1269,4 @@ class rdesigneur:
for j in range( i[1], i[2] ):
moose.connect( i[3], 'requestOut', chemVec[j], chemFieldSrc)
msg = moose.connect( i[3], 'output', elObj, elecFieldDest )
+
diff --git a/moose-core/python/rdesigneur/rdesigneurProtos.py b/moose-core/python/rdesigneur/rdesigneurProtos.py
index 8dd7f0197835c5adf30f89173165ca79b4d13fea..a0c3f956585ce4b14bf681926b8ea838faeeaa99 100644
--- a/moose-core/python/rdesigneur/rdesigneurProtos.py
+++ b/moose-core/python/rdesigneur/rdesigneurProtos.py
@@ -302,7 +302,7 @@ def addSpineProto( name = 'spine',
chanList = (),
caTau = 0.0
):
- assert( moose.exists( parent ) )
+ assert moose.exists( parent ), "%s must exists" % parent
spine = moose.Neutral( parent + '/' + name )
shaft = buildCompt( spine, 'shaft', shaftLen, shaftDia, 0.0, RM, RA, CM )
head = buildCompt( spine, 'head', headLen, headDia, shaftLen, RM, RA, CM )
diff --git a/moose-core/randnum/RNG.h b/moose-core/randnum/RNG.h
index c5e8afe24d0e2038a6f332f7a70f0e78d38b9b8e..09dbdf05a691d74a36cded4f7012bb33388da654 100644
--- a/moose-core/randnum/RNG.h
+++ b/moose-core/randnum/RNG.h
@@ -20,27 +20,27 @@
#define __RNG_INC
#ifdef USE_BOOST
+
#include <boost/random.hpp>
-#include <boost/random/uniform_int.hpp>
+#include <boost/random/uniform_01.hpp>
-#if BOOST_RANDOM_DEVICE_EXISTS
+#if defined(BOOST_RANDOM_DEVICE_EXISTS)
#include <boost/random/random_device.hpp>
-#endif /* ----- BOOST_RANDOM_DEVICE_EXISTS ----- */
-
+#endif // BOOST_RANDOM_DEVICE_EXISTS
#else /* ----- not USE_BOOST ----- */
-
-#ifdef ENABLE_CPP11
-#include <random>
-#elif USE_GSL /* ----- not ENABLE_CPP11 and using GSL ----- */
#include <ctime>
-#include <gsl/gsl_rng.h>
-#endif /* ----- not ENABLE_CPP11 ----- */
-
+#include "randnum.h"
#endif /* ----- not USE_BOOST ----- */
#include <limits>
#include <iostream>
+#ifdef ENABLE_CPP11
+#include <random>
+#endif
+
+using namespace std;
+
namespace moose {
/*
@@ -57,17 +57,16 @@ class RNG
RNG () /* constructor */
{
// Setup a random seed if possible.
-#ifdef ENABLE_CPP11
- std::random_device rd;
- setSeed( rd() );
-#elif defined(USE_BOOST) && defined(BOOST_RANDOM_DEVICE_EXISTS)
+#if defined(USE_BOOST)
+#if defined(BOOST_RANDOM_DEVICE_EXISTS)
boost::random::random_device rd;
setSeed( rd() );
-#elif USE_GSL
- gsl_r_ = gsl_rng_alloc( gsl_rng_default );
- gsl_rng_set( gsl_r_, time(NULL) );
-#else /* ----- not ENABLE_CPP11 ----- */
-
+#endif
+#elif defined(ENABLE_CPP11)
+ std::random_device rd;
+ setSeed( rd() );
+#else
+ mtseed( time(NULL) );
#endif /* ----- not ENABLE_CPP11 ----- */
}
@@ -75,11 +74,6 @@ class RNG
~RNG () /* destructor */
{
-#if defined(USE_BOOST) || defined(ENABLE_CPP11)
-#else
- gsl_rng_free( gsl_r_ );
-#endif
-
}
/* ==================== ACCESSORS ======================================= */
@@ -89,15 +83,13 @@ class RNG
}
/* ==================== MUTATORS ======================================= */
- void setSeed( const T seed )
+ void setSeed( const unsigned long int seed )
{
-#if defined(USE_BOOST) || defined(ENABLE_CPP11)
seed_ = seed;
+#if defined(USE_BOOST) || defined(ENABLE_CPP11)
rng_.seed( seed_ );
-#elif USE_GSL
- gsl_rng_set(gsl_r_, seed );
-#else
- std::srand( seed_ );
+#else
+ mtseed( seed_ );
#endif
}
@@ -105,17 +97,14 @@ class RNG
* @brief Generate a uniformly distributed random number between a and b.
*
* @param a Lower limit (inclusive)
- * @param b Upper limit (exclusive).
+ * @param b Upper limit (inclusive).
*/
T uniform( const T a, const T b)
{
- size_t maxInt = std::numeric_limits<int>::max();
#if defined(USE_BOOST) || defined(ENABLE_CPP11)
- return ( (b - a ) * (T)dist_( rng_ ) / maxInt ) + a;
-#elif USE_GSL
- return ( (b -a ) * (T)gsl_rng_get( gsl_r_ ) / gsl_rng_max( gsl_r_ ) + a );
+ return ( b - a ) * dist_( rng_ ) + a;
#else
- return (b-a) * (T)rand() / RAND_MAX + a;
+ return (b-a) * mtrand() + a;
#endif
}
@@ -127,12 +116,10 @@ class RNG
*/
T uniform( void )
{
-#if defined(USE_BOOST) || defined(ENABLE_CPP11)
- return (T)dist_( rng_ ) / std::numeric_limits<int>::max();
-#elif USE_GSL
- return (T)gsl_rng_uniform( gsl_r_ );
+#if defined(USE_BOOST) || defined(ENABLE_CPP11)
+ return dist_( rng_ );
#else
- return (T)rand( ) / RAND_MAX;
+ return mtrand();
#endif
}
@@ -144,12 +131,10 @@ class RNG
#if USE_BOOST
boost::random::mt19937 rng_;
- boost::random::uniform_int_distribution<> dist_;
+ boost::random::uniform_01<T> dist_;
#elif ENABLE_CPP11
std::mt19937 rng_;
- std::uniform_int_distribution<> dist_;
-#else /* ----- not ENABLE_CPP11 ----- */
- gsl_rng* gsl_r_;
+ std::uniform_real_distribution<> dist_;
#endif /* ----- not ENABLE_CPP11 ----- */
}; /* ----- end of template class RNG ----- */
diff --git a/moose-core/scheduling/Clock.cpp b/moose-core/scheduling/Clock.cpp
index b464b5adc20f7072a352dd20604fd339a283fed2..a90cb7c9dbb10d558bb5f9425cc4819886f54caf 100644
--- a/moose-core/scheduling/Clock.cpp
+++ b/moose-core/scheduling/Clock.cpp
@@ -307,7 +307,7 @@ const Cinfo* Clock::initCinfo()
"Name", "Clock",
"Author", "Upinder S. Bhalla, Nov 2013, NCBS",
"Description",
- "Clock: Clock class. Handles sequencing of operations in simulations."
+
"Every object scheduled for operations in MOOSE is connected to one"
"of the 'Tick' entries on the Clock.\n"
"The Clock manages 32 'Ticks', each of which has its own dt,"
@@ -413,9 +413,9 @@ const Cinfo* Clock::initCinfo()
" Gsolve 16 0.1\n"
" Ksolve 16 0.1\n"
" Stats 17 0.1\n"
-
" Table2 18 1\n"
- " Streamer 29 2\n"
+ " Streamer 19 10\n"
+
" HDF5DataWriter 30 1\n"
" HDF5WriterBase 30 1\n"
" NSDFWriter 30 1\n"
@@ -591,6 +591,7 @@ void Clock::setTickDt( unsigned int i, double v )
}
for ( unsigned int j = 0; j < numTicks; ++j )
numUsed += ( ticks_[j] != 0 );
+
if ( numUsed == 0 )
{
dt_ = v;
@@ -897,7 +898,7 @@ void Clock::buildDefaultTick()
defaultTick_["Stats"] = 17;
defaultTick_["Table2"] = 18;
- defaultTick_["Streamer"] = 29;
+ defaultTick_["Streamer"] = 19;
defaultTick_["HDF5DataWriter"] = 30;
defaultTick_["HDF5WriterBase"] = 30;
defaultTick_["NSDFWriter"] = 30;
@@ -962,9 +963,9 @@ void Clock::buildDefaultTick()
defaultDt_[5] = 50.0e-6;
defaultDt_[6] = 50.0e-6;
defaultDt_[7] = 50.0e-6;
- defaultDt_[8] = 1.0e-4; // For the tables for electrical calculations
- defaultDt_[9] = 0.0; // Not assigned
- defaultDt_[10] = 0.01; // For diffusion.
+ defaultDt_[8] = 1.0e-4; // For the tables for electrical calculations
+ defaultDt_[9] = 0.0; // Not assigned
+ defaultDt_[10] = 0.01; // For diffusion.
defaultDt_[11] = 0.1;
defaultDt_[12] = 0.1;
defaultDt_[13] = 0.1;
@@ -972,9 +973,10 @@ void Clock::buildDefaultTick()
defaultDt_[15] = 0.1;
defaultDt_[16] = 0.1;
defaultDt_[17] = 0.1;
- defaultDt_[18] = 1; // For tables for chemical calculations.
- // 19-28 are not assigned.
- defaultDt_[29] = 10; // For Streamer
+ defaultDt_[18] = 1; // For tables for chemical calculations.
+ defaultDt_[19] = 10; // For Streamer
+
+ // 20-29 are not assigned.
defaultDt_[30] = 1; // For the HDF writer
defaultDt_[31] = 0.01; // For the postmaster.
}
diff --git a/moose-core/scripts/setup_subha.py b/moose-core/scripts/setup.cygwin.py
similarity index 100%
rename from moose-core/scripts/setup_subha.py
rename to moose-core/scripts/setup.cygwin.py
diff --git a/moose-core/shell/Shell.cpp b/moose-core/shell/Shell.cpp
index b17d6e6e67db20f8f85d1bddc97c665f85f34a00..85aca3e4442e2fdc9744da48e78832ee524a86dd 100644
--- a/moose-core/shell/Shell.cpp
+++ b/moose-core/shell/Shell.cpp
@@ -8,6 +8,8 @@
**********************************************************************/
#include <string>
+#include <algorithm>
+
using namespace std;
@@ -381,17 +383,9 @@ bool isDoingReinit()
void Shell::doReinit( )
{
-#ifdef ENABLE_LOGGER
- clock_t t = clock();
- cout << logger.dumpStats(0);
-#endif
Id clockId( 1 );
SetGet0::set( clockId, "reinit" );
-#ifdef ENABLE_LOGGER
- float time = (float(clock() - t)/CLOCKS_PER_SEC);
- logger.initializationTime.push_back(time);
-#endif
}
void Shell::doStop( )
@@ -404,6 +398,14 @@ void Shell::doStop( )
void Shell::doSetClock( unsigned int tickNum, double dt )
{
LookupField< unsigned int, double >::set( ObjId( 1 ), "tickDt", tickNum, dt );
+
+ // FIXME:
+ // HACK: If clock 18 is being updated, make sure that clock 19 (streamer is also
+ // updated with correct dt (10 or 100*dt). This is bit hacky.
+ if( tickNum == 18 )
+ LookupField< unsigned int, double >::set( ObjId( 1 ), "tickDt"
+ , tickNum + 1, max( 100 * dt, 10.0 )
+ );
}
void Shell::doUseClock( string path, string field, unsigned int tick )
diff --git a/moose-core/tests/issues/issue_124.py b/moose-core/tests/issues/issue_124.py
new file mode 100644
index 0000000000000000000000000000000000000000..d4c377726da243976de3bc4d655be32d8312606a
--- /dev/null
+++ b/moose-core/tests/issues/issue_124.py
@@ -0,0 +1,32 @@
+import moose
+print(( 'Using moose form %s' % moose.__file__ ))
+
+
+def main():
+ solver = "gssa"
+ moose.Neutral('/model')
+ moose.CubeMesh('/model/kinetics')
+ moose.Pool('/model/kinetics/A')
+
+ #delete if exists
+ if ( moose.exists( 'model/kinetics/stoich' ) ):
+ moose.delete( '/model/kinetics/stoich' )
+ moose.delete( '/model/kinetics/ksolve' )
+
+ #create solver
+ compt = moose.element( '/model/kinetics' )
+ ksolve = moose.Gsolve( '/model/kinetics/ksolve' )
+ stoich = moose.Stoich( '/model/kinetics/stoich' )
+ stoich.compartment = compt
+ stoich.ksolve = ksolve
+ stoich.path = "/model/kinetics/##"
+ print(" before reinit")
+ moose.reinit()
+ print(" After reinit")
+ moose.start( 10 )
+ print( "Done" )
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main()
+
diff --git a/moose-core/tests/issues/issue_93.py b/moose-core/tests/issues/issue_93.py
index 11e61e8556168165673f973d5cca52a3e6feb091..d804a342dc5733ff7d7f5df80d2af7887a9fdb32 100644
--- a/moose-core/tests/issues/issue_93.py
+++ b/moose-core/tests/issues/issue_93.py
@@ -3,10 +3,13 @@
import numpy as np
import pylab as pl
import moose
+import os
import sys
dt = 10e-6
+d = os.path.split( os.path.abspath( __file__ ) )[0]
+
def loadAndRun(solver=True):
simtime = 500e-3
model = moose.loadModel('../data/h10.CNG.swc', '/cell')
@@ -36,6 +39,8 @@ def loadAndRun(solver=True):
return vec
def main( ):
+ print( '[INFO] See the detailed issue in %s/hsolve' % d )
+ quit()
eeVec = loadAndRun( False )
hsolveVec = loadAndRun( True )
clk = moose.Clock( '/clock' )
diff --git a/moose-core/tests/python/test_ksolve.py b/moose-core/tests/python/test_ksolve.py
index e8d84f62eade3c2ae8ccc6b1cf5cf2e0a30bbe17..1b6c210af793091083f1c8d0fcb08062b7201833 100644
--- a/moose-core/tests/python/test_ksolve.py
+++ b/moose-core/tests/python/test_ksolve.py
@@ -28,10 +28,6 @@ for r in range( 10 ):
pools += [ a1, a2, b1, b2 ]
ksolve = moose.Ksolve( '/compt/ksolve' )
-try:
- ksolve.method = 'rk4'
-except Exception as e:
- pass
stoich = moose.Stoich( '/compt/stoich' )
stoich.compartment = compt
stoich.ksolve = ksolve
diff --git a/moose-core/tests/python/test_streamer.py b/moose-core/tests/python/test_streamer.py
index eeb8145d84012a2fa2813512c277e325e2663410..3c16b76c97bac35d72e8a2ba1cfdf0c3eb4080f2 100644
--- a/moose-core/tests/python/test_streamer.py
+++ b/moose-core/tests/python/test_streamer.py
@@ -87,9 +87,9 @@ def test( ):
# Now create a streamer and use it to write to a stream
st = moose.Streamer( '/compt/streamer' )
- st.outfile = os.path.join( os.getcwd(), 'temp.csv' )
+ st.outfile = os.path.join( os.getcwd(), 'temp.npy' )
print(("outfile set to: %s " % st.outfile ))
- assert st.outfile == os.path.join( os.getcwd(), 'temp.csv' ), st.outfile
+ assert st.outfile == os.path.join( os.getcwd(), 'temp.npy' ), st.outfile
st.addTable( tabA )
st.addTables( [ tabB, tabC ] )
@@ -104,10 +104,16 @@ def test( ):
# Now read the table and verify that we have written
print( '[INFO] Reading file %s' % outfile )
- data = np.loadtxt(outfile, skiprows=1 )
+ if 'csv' in outfile:
+ data = np.loadtxt(outfile, skiprows=1 )
+ else:
+ data = np.load( outfile )
# Total rows should be 58 (counting zero as well).
- print(data)
- assert data.shape >= (58,4), data.shape
+ # print(data)
+ # print( data.dtype )
+ time = data['time']
+ print( time )
+ assert data.shape >= (58,), data.shape
print( '[INFO] Test 2 passed' )
def main( ):
diff --git a/moose-core/utility/cnpy.cpp b/moose-core/utility/cnpy.cpp
index 96b4a7e4ac750d3bda4bc2ae2999b59ea17f379c..60d7717598bdba86c73da564d704e55d8a5d3200 100644
--- a/moose-core/utility/cnpy.cpp
+++ b/moose-core/utility/cnpy.cpp
@@ -18,6 +18,7 @@
#include "cnpy.hpp"
#include <cstring>
+#include "print_function.hpp"
using namespace std;
@@ -35,8 +36,8 @@ char BigEndianTest() {
char map_type(const std::type_info& t)
{
if(t == typeid(float) ) return 'f';
- if(t == typeid(double) ) return 'f';
- if(t == typeid(long double) ) return 'f';
+ if(t == typeid(double) ) return 'd';
+ if(t == typeid(long double) ) return 'd';
if(t == typeid(int) ) return 'i';
if(t == typeid(char) ) return 'i';
@@ -80,16 +81,10 @@ void split(vector<string>& strs, string& input, const string& pat)
*
* @return true if file is sane, else false.
*/
-bool is_valid_numpy_file( const string& npy_file )
+bool is_valid_numpy_file( FILE* fp )
{
+ assert( fp );
char buffer[__pre__size__];
- FILE* fp = NULL;
- fp = fopen( npy_file.c_str(), "r" );
- if(!fp)
- {
- LOG( moose::warning, "Can't open " << npy_file );
- return false;
- }
fread( buffer, sizeof(char), __pre__size__, fp );
bool equal = true;
// Check for equality
@@ -136,11 +131,19 @@ void change_shape_in_header( const string& filename
// Always open file in r+b mode. a+b mode always append at the end.
FILE* fp = fopen( filename.c_str(), "r+b" );
+ if( ! fp )
+ {
+ moose::showWarn( "Failed to open " + filename );
+ return;
+ }
+
parse_header( fp, header );
size_t shapePos = header.find( "'shape':" );
size_t lbrac = header.find( '(', shapePos );
size_t rbrac = header.find( ')', lbrac );
+ assert( lbrac > shapePos );
+ assert( rbrac > lbrac );
string prefixHeader = header.substr( 0, lbrac + 1 );
string postfixHeader = header.substr( rbrac );
@@ -154,7 +157,7 @@ void change_shape_in_header( const string& filename
for (size_t i = 0; i < tokens.size(); i++)
newShape += moose::toString( atoi( tokens[i].c_str() ) + data_len/numcols ) + ",";
- string newHeader = prefixHeader + newShape + postfixHeader;
+ string newHeader = prefixHeader + newShape + postfixHeader + "\n";
if( newHeader.size() < header.size() )
{
cout << "Warn: Modified header can not be smaller than old header" << endl;
diff --git a/moose-core/utility/cnpy.hpp b/moose-core/utility/cnpy.hpp
index b184f39430bcea630acbc27306b275bca11e3ba6..2a824adbcbf318ee0662a3530e9c02dc3fb975cc 100644
--- a/moose-core/utility/cnpy.hpp
+++ b/moose-core/utility/cnpy.hpp
@@ -65,7 +65,7 @@ void split(vector<string>& strs, string& input, const string& pat);
*
* @return true if file is sane, else false.
*/
-bool is_valid_numpy_file( const string& npy_file );
+bool is_valid_numpy_file( FILE* fp );
/**
* @brief Parser header from a numpy file. Store it in vector.
@@ -182,7 +182,7 @@ void save_numpy(
FILE* fp = fopen( outfile.c_str(), "wb" );
if( NULL == fp )
{
- LOG( moose::warning, "Could not open file " << outfile );
+ moose::showWarn( "Could not open file " + outfile );
return;
}
write_header<T>( fp, colnames, shape, version );
@@ -191,19 +191,31 @@ void save_numpy(
else /* Append mode. */
{
// Do a sanity check if file is really a numpy file.
- if(! is_valid_numpy_file( outfile ) )
+ FILE* fp = fopen( outfile.c_str(), "r" );
+ if( ! fp )
{
- LOG( moose::warning,
- outfile << " is not a valid numpy file"
- << " I am not goind to write to it"
- );
+ moose::showError( "Can't open " + outfile + " to validate" );
return;
}
+ else if(! is_valid_numpy_file( fp ) )
+ {
+ moose::showWarn( outfile + " is not a valid numpy file"
+ + " I am not goind to write to it"
+ );
+ return;
+ }
+ if( fp )
+ fclose( fp );
// And change the shape in header.
change_shape_in_header( outfile, vec.size(), colnames.size() );
}
FILE* fp = fopen( outfile.c_str(), "ab" );
+ if( NULL == fp )
+ {
+ moose::showWarn( "Could not open " + outfile + " to write " );
+ return;
+ }
fwrite( &vec[0], sizeof(T), vec.size(), fp );
fclose( fp );
diff --git a/moose-core/utility/print_function.hpp b/moose-core/utility/print_function.hpp
index 38f264534ed92b41ae923e5a833563044a995a3f..415d36ae6425d262e2df4955917230177f62dd23 100644
--- a/moose-core/utility/print_function.hpp
+++ b/moose-core/utility/print_function.hpp
@@ -60,15 +60,11 @@ namespace moose {
* @brief Enumerate type for debug and log.
*/
enum serverity_level_ {
- trace, debug, info
- , warning, fixme
- , error, fatal, failed
+ trace, debug, info , warning, fixme , error, fatal, failed
};
static string levels_[9] = {
- "TRACE", "DEBUG", "INFO", "LOG"
- , "WARNING", "FIXME"
- , "ERROR", "FATAL", "FAILED"
+ "TRACE", "DEBUG", "INFO", "WARNING", "FIXME" , "ERROR", "FATAL", "FAILED"
};
/*
@@ -201,6 +197,24 @@ namespace moose {
cout << ss.str() << endl;
}
+ /*
+ * Wrapper function around __dump__
+ */
+ inline void showInfo( string msg )
+ {
+ moose::__dump__( msg, moose::info );
+ }
+
+ inline void showWarn( string msg )
+ {
+ moose::__dump__(msg, moose::warning );
+ }
+
+ inline void showError( string msg )
+ {
+ moose::__dump__( msg, moose::error );
+ }
+
/**
* @brief This macro only expands when not compiling for release.
*
diff --git a/moose-core/utility/setupenv.cpp b/moose-core/utility/setupenv.cpp
index 1dc7f417ef1046749ea995c596b4756ca12ee989..4410f883f879e7b530cfb16ba9cff739596fd9b2 100644
--- a/moose-core/utility/setupenv.cpp
+++ b/moose-core/utility/setupenv.cpp
@@ -37,73 +37,75 @@ using namespace std;
extern unsigned getNumCores();
-const map<string, string>& getArgMap()
-{
- static map<string, string> argmap;
- if (argmap.empty()){
- char * verbosity = getenv("VERBOSITY");
- if (verbosity != NULL){
- argmap.insert(pair<string, string>("VERBOSITY", string(verbosity)));
- } else {
- argmap.insert(pair<string, string>("VERBOSITY", "0"));
- }
- char * isSingleThreaded = getenv("SINGLETHREADED");
- if (isSingleThreaded != NULL){
- argmap.insert(pair<string, string>("SINGLETHREADED", string(isSingleThreaded)));
- }
- else {
- argmap.insert(pair<string, string>("SINGLETHREADED", "0"));
- }
- char * isInfinite = getenv("INFINITE");
- if (isInfinite != NULL){
- argmap.insert(pair<string, string>("INFINITE", string(isInfinite)));
- }
- // else {
- // argmap.insert(pair<string, string>("INFINITE", "0"));
- // }
-
- char * numCores = getenv("NUMCORES");
- if (numCores != NULL){
- argmap.insert(pair<string, string>("NUMCORES", string(numCores)));
- } else {
- unsigned int cores = getNumCores();
- stringstream s;
- s << cores;
- argmap.insert(pair<string, string>("NUMCORES", s.str()));
- }
- char * numNodes = getenv("NUMNODES");
- if (numNodes != NULL){
- argmap.insert(pair<string, string>("NUMNODES", string(numNodes)));
- } // else {
- // argmap.insert(pair<string, string>("NUMNODES", "1"));
- // }
- char * numProcessThreads = getenv("NUMPTHREADS");
- if (numProcessThreads != NULL){
- argmap.insert(pair<string, string>("NUMPTHREADS", string(numProcessThreads)));
+namespace moose {
+ const map<string, string>& getArgMap()
+ {
+ static map<string, string> argmap;
+ if (argmap.empty()){
+ char * verbosity = getenv("VERBOSITY");
+ if (verbosity != NULL){
+ argmap.insert(pair<string, string>("VERBOSITY", string(verbosity)));
+ } else {
+ argmap.insert(pair<string, string>("VERBOSITY", "0"));
+ }
+ char * isSingleThreaded = getenv("SINGLETHREADED");
+ if (isSingleThreaded != NULL){
+ argmap.insert(pair<string, string>("SINGLETHREADED", string(isSingleThreaded)));
+ }
+ else {
+ argmap.insert(pair<string, string>("SINGLETHREADED", "0"));
+ }
+ char * isInfinite = getenv("INFINITE");
+ if (isInfinite != NULL){
+ argmap.insert(pair<string, string>("INFINITE", string(isInfinite)));
+ }
+ // else {
+ // argmap.insert(pair<string, string>("INFINITE", "0"));
+ // }
+
+ char * numCores = getenv("NUMCORES");
+ if (numCores != NULL){
+ argmap.insert(pair<string, string>("NUMCORES", string(numCores)));
+ } else {
+ unsigned int cores = getNumCores();
+ stringstream s;
+ s << cores;
+ argmap.insert(pair<string, string>("NUMCORES", s.str()));
+ }
+ char * numNodes = getenv("NUMNODES");
+ if (numNodes != NULL){
+ argmap.insert(pair<string, string>("NUMNODES", string(numNodes)));
+ } // else {
+ // argmap.insert(pair<string, string>("NUMNODES", "1"));
+ // }
+ char * numProcessThreads = getenv("NUMPTHREADS");
+ if (numProcessThreads != NULL){
+ argmap.insert(pair<string, string>("NUMPTHREADS", string(numProcessThreads)));
+ }
+ char * doQuit = getenv("QUIT");
+ if (doQuit != NULL){
+ argmap.insert(pair<string, string>("QUIT", string(doQuit)));
+ } // else {
+ // argmap.insert(pair<string, string>("QUIT", "0"));
+ // }
+ char * doUnitTests = getenv("DOUNITTESTS");
+ if (doUnitTests != NULL){
+ argmap.insert(pair<string, string>("DOUNITTESTS", string(doUnitTests)));
+ } // else {
+ // argmap.insert(pair<string, string>("DOUNITTESTS", "0"));
+ // }
+ char * doRegressionTests = getenv("DOREGRESSIONTESTS");
+ if (doRegressionTests != NULL){
+ argmap.insert(pair<string, string>("DOREGRESSIONTESTS", string(doRegressionTests)));
+ } // else {
+ // argmap.insert(pair<string, string>("DOREGRESSIONTESTS", "0"));
+ // }
+
}
- char * doQuit = getenv("QUIT");
- if (doQuit != NULL){
- argmap.insert(pair<string, string>("QUIT", string(doQuit)));
- } // else {
- // argmap.insert(pair<string, string>("QUIT", "0"));
- // }
- char * doUnitTests = getenv("DOUNITTESTS");
- if (doUnitTests != NULL){
- argmap.insert(pair<string, string>("DOUNITTESTS", string(doUnitTests)));
- } // else {
- // argmap.insert(pair<string, string>("DOUNITTESTS", "0"));
- // }
- char * doRegressionTests = getenv("DOREGRESSIONTESTS");
- if (doRegressionTests != NULL){
- argmap.insert(pair<string, string>("DOREGRESSIONTESTS", string(doRegressionTests)));
- } // else {
- // argmap.insert(pair<string, string>("DOREGRESSIONTESTS", "0"));
- // }
-
+ return argmap;
}
- return argmap;
-}
+}
//
diff --git a/moose-core/utility/testing_macros.hpp b/moose-core/utility/testing_macros.hpp
index ac99462ed373d2c2b66db4e416d7db1f0efd3e3c..99881aec48c355406014b8d314295f1d3feb39c2 100644
--- a/moose-core/utility/testing_macros.hpp
+++ b/moose-core/utility/testing_macros.hpp
@@ -22,7 +22,7 @@
#include <sstream>
#include <exception>
#include <iostream>
-#include <exception>
+#include <stdexcept>
#include <limits>
#include <cmath>
@@ -118,7 +118,7 @@ static ostringstream assertStream;
if( !(condition) ) {\
assertStream.str(""); \
assertStream << msg << endl; \
- throw runtime_error( assertStream.str() );\
+ throw std::runtime_error( assertStream.str() );\
}
#define ASSERT_FALSE( condition, msg) \
@@ -126,7 +126,7 @@ static ostringstream assertStream;
assertStream.str(""); \
assertStream.precision( 9 ); \
assertStream << msg << endl; \
- throw runtime_error(assertStream.str()); \
+ throw std::runtime_error(assertStream.str()); \
}
#define ASSERT_LT( a, b, msg) \
@@ -134,7 +134,7 @@ static ostringstream assertStream;
assertStream.str(""); \
assertStream.precision( 9 ); \
assertStream << msg; \
- throw runtime_error( assertStream.str() ); \
+ throw std::runtime_error( assertStream.str() ); \
#define ASSERT_EQ(a, b, token) \
if( ! doubleEq((a), (b)) ) { \
@@ -143,7 +143,7 @@ static ostringstream assertStream;
LOCATION(assertStream) \
assertStream << "Expected " << a << ", received " << b << endl; \
assertStream << token << endl; \
- throw runtime_error(assertStream.str()); \
+ throw std::runtime_error(assertStream.str()); \
}
#define ASSERT_DOUBLE_EQ(token, a, b) \
@@ -153,7 +153,7 @@ static ostringstream assertStream;
assertStream << "Expected " << b << ", received " << a << endl; \
assertStream << token; \
moose::__dump__(assertStream.str(), moose::failed); \
- throw runtime_error( "float equality test failed" ); \
+ throw std::runtime_error( "float equality test failed" ); \
}
#define ASSERT_NEQ(a, b, token) \
@@ -162,7 +162,7 @@ static ostringstream assertStream;
LOCATION(assertStream); \
assertStream << "Not expected " << a << endl; \
assertStream << token << endl; \
- throw runtime_error(assertStream.str()); \
+ throw std::runtime_error(assertStream.str()); \
}
diff --git a/moose-core/utility/utility.h b/moose-core/utility/utility.h
index b0cb13f26d358a29679e162ffda7a4f826b9da07..ef5ef712b4d029a3d1cf94abc2d1efcd1e61deef 100644
--- a/moose-core/utility/utility.h
+++ b/moose-core/utility/utility.h
@@ -30,14 +30,28 @@
// Code:
#ifndef _UTILITY_H
+#include "strutil.h"
+namespace moose {
-char shortType(std::string type);
-char innerType(char typecode);
-char shortFinfo(std::string ftype);
+ char shortType(std::string type);
+ char innerType(char typecode);
+ char shortFinfo(std::string ftype);
+ const map<std::string, std::string>& getArgMap();
+
+ /**
+ * @brief Givem path of MOOSE element, return its name. It's behaviour is
+ * like `basename` of unix command e.g. /a/b/c --> c
+ *
+ * @return
+ */
+ inline string basename( const string& path )
+ {
+ return path.substr( path.find_last_of('/') + 1 );
+ }
+
+}
-#include "strutil.h"
-const map<std::string, std::string>& getArgMap();
#endif // !_UTILITY_H