diff --git a/moose-core/.travis.yml b/moose-core/.travis.yml
index e69122259038e110c41ef471f75be1f04effb3c0..c4aa5e91786a7e86eee00c2f24b8972b7a4bc1be 100644
--- a/moose-core/.travis.yml
+++ b/moose-core/.travis.yml
@@ -7,7 +7,10 @@ os:
- linux
- osx
-osx_image: xcode10
+matrix:
+ include:
+ - os : osx
+ osx_image: xcode10
notifications:
email:
diff --git a/moose-core/.travis/travis_prepare_osx.sh b/moose-core/.travis/travis_prepare_osx.sh
index d8aa29a1719ebd80e12a0e5b2b6920313cf1cceb..d56638ed70f802230d570697cc3d3dc3fdac8bdd 100755
--- a/moose-core/.travis/travis_prepare_osx.sh
+++ b/moose-core/.travis/travis_prepare_osx.sh
@@ -20,9 +20,9 @@
set -o nounset # Treat unset variables as an error
set +e
#rvm get head
-#brew update
-#brew outdated cmake || brew install cmake
-brew install gsl
+brew update || echo "failed to update"
+brew outdated cmake || brew install cmake
+brew install gsl || brew upgrade gsl
brew install hdf5
brew install python
brew install numpy
diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index ec094e5877f7b3709101ccf45242d0240fff65d9..b30ca55de3a35154d864570dbc974bf413b51c1b 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -97,7 +97,7 @@ else()
message(STATUS "Building for Release/No unit tests.")
set(CMAKE_BUILD_TYPE Release)
add_definitions(-UDO_UNIT_TESTS -O3 -DDISABLE_DEBUG)
-
+
# DO NOT Treat all warnings as errors. With some compilers and newer versions
# this often causes headache.
# add_definitions(-Werror)
@@ -353,7 +353,7 @@ if(SYSTEM_SHARED_LIBS)
list(REMOVE_DUPLICATES SYSTEM_SHARED_LIBS)
endif( )
-# cmake --help-policy CMP0042. Also in pymoose/CMakeLists.txt
+# cmake --help-policy CMP0042. Also in pymoose/CMakeLists.txt
# More details:
# https://gitlab.kitware.com/cmake/community/wikis/doc/cmake/RPATH-handling
# especially section 'Mac OS X and the RPATH'
@@ -528,8 +528,8 @@ foreach( _py_script ${PY_SCRIPTS} )
file( READ ${_py_script} pytext)
string(MD5 _md5 "${pytext}")
set(TGT_NAME "${_py_name}-${_md5}" )
- set(PYLINT_OPTIONS --disable=no-member --disable=no-name-in-module
- --disable=invalid-unary-operand-type
+ set(PYLINT_OPTIONS --disable=no-member --disable=no-name-in-module
+ --disable=invalid-unary-operand-type
--disable=import-error
--disable=no-method-argument
)
diff --git a/moose-core/INSTALL.md b/moose-core/INSTALL.md
index 6f2272b2c130c9e9b02516dffe83cb31a6cd17fc..63af4f3a9ce0ff4619203d14cf1a768e764ae875 100644
--- a/moose-core/INSTALL.md
+++ b/moose-core/INSTALL.md
@@ -1,43 +1,22 @@
-# Pre-built packages
-
-## Linux
-
-Use our repositories hosted at [Open Build Service](http://build.opensuse.org).
-We have packages for Debian, Ubuntu, CentOS, Fedora, OpenSUSE/SUSE, RHEL,
-Scientific Linux. Visit the following page for instructions.
-
-https://software.opensuse.org/download.html?project=home:moose&package=moose
-
-## MacOSX
-
-MOOSE is available via [homebrew](http://brew.sh).
-
- $ brew install homebrew/science/moose
-
-
# Building MOOSE from source
-To build `MOOSE` from source, you can either use `cmake` (recommended) or GNU `make` based flow.
+To build `MOOSE` from source, you need `cmake`.
Download the latest source code of moose from github.
- $ git clone -b master https://github.com/BhallaLab/moose-core
+ $ git clone -b master https://github.com/BhallaLab/moose-core --depth 50
## Install dependencies
-For moose-core:
-
- gsl-1.16 or higher.
- libhdf5-dev (optional)
- python-dev
- python-numpy
-On Ubuntu-12.04 or higher, these can be installed with:
+On Ubuntu-14.04 or higher, these can be installed with:
sudo apt-get install python-dev python-numpy libhdf5-dev cmake libgsl0-dev g++
-__NOTE__ : On Ubuntu 12.04, gsl version is 1.15. You should skip `libgsl0-dev` install gsl-1.16 or higher manually.
-
SBML support is enabled by installing [python-libsbml](http://sbml.org/Software/libSBML/docs/python-api/libsbml-installation.html). Alternatively, it can be installed by using `python-pip`
$ sudo pip install python-libsbml
@@ -48,90 +27,24 @@ SBML support is enabled by installing [python-libsbml](http://sbml.org/Software/
$ mkdir _build
$ cd _build
$ cmake ..
- $ make
- $ ctest --output-on-failure
+ $ make -j3
+ $ ctest -j3 --output-on-failure
-This will build moose and its python extentions, `ctest` will run few tests to
-check if build process was successful.
+This will build moose, `ctest` will run few tests to check if build process was successful.
To install MOOSE into non-standard directory, pass additional argument `-DCMAKE_INSTALL_PREFIX=path/to/install/dir` to cmake.
### Python3
-You just need to one command in previous set of instructions to following
-
cmake -DPYTHON_EXECUTABLE=/opt/bin/python3 ..
### Install
$ sudo make install
-## Using gnu-make
-
-__This may or may not work (not maintained by packager)__
-
-You may need to inform make of C++ include directories and library directories
-if your installed packages are at non-standard location. For example, if your
-have libsbml installed in `/opt/libsbml` and the header files are located in
-`/opt/libsbml/include` and lib files are located in `/opt/libsbml/lib`, you can
-set the environment variables `CXXFLAGS` and `LDFLAGS` to include these before
-calling make:
-
- export CXXFLAGS= -I/opt/libsbml/include
- export LDFLAGS= -L/opt/libsbml/lib
-
-
-### Release build:
-
- cd moose
- make BUILD=release
-
-### Debug build:
-
- cd moose
- make BUILD=debug
-
-### Python 3K
-
-By default, MOOSE is built for Python 2. In case you want to build MOOSE for
-Python 3K, you need to pass the additional flag:
-
- PYTHON=3
-
-like:
-
- make BUILD=release PYTHON=3
-
-## Installation:
-
-For system-wide installation you can run:
-
- sudo make install
-
## Post installation
Now you can import moose in a Python script or interpreter with the statement:
import moose
-
-If you have installed the GUI dependencies below for running the graphical user
-interface, then you can run the GUI by double-clicking on the desktop icon or
-via the main-menu. The squid axon tutorial/demo is also accessible via these
-routes.
-
-## Local-installation
-
-If you do not have permission to install it in system directories, you can let
-it be where it was built or copy the `python` subdirectory of MOOSE source tree
-to a location of your choice and add the path to your PYTHONPATH environment
-variable. Suppose you have a ~/lib directory where you keep all your locally
-built libraries, do:
-
- cp -r {moose-source-directory}/python ~/lib/
-
-and add this to your .bashrc file (if you use bash shell):
-
- export PYTHONPATH="$HOME/lib/python":"$PYTHONPATH"
-
-For other shells, look up your shell's manual to find out how to set environment
-variable in it.
+ moose.test() # will take time. Not all tests will pass.
diff --git a/moose-core/basecode/ObjId.cpp b/moose-core/basecode/ObjId.cpp
index 9e846603ff806d71c520b3b1c79e2464533659ca..9c1c823139e778920457ddc6093d4b3d027aee6a 100644
--- a/moose-core/basecode/ObjId.cpp
+++ b/moose-core/basecode/ObjId.cpp
@@ -17,33 +17,33 @@
// Doesn't know how to deal with off-node bad fields.
bool ObjId::bad() const
{
- Element* elm = id.element();
- return ( elm == 0 ||
- dataIndex == BADINDEX ||
- fieldIndex == BADINDEX ||
- dataIndex >= elm->numData()
- /*
- * We have a bit of a problem here. The FieldElement can exist
- * with zero fields, and is invalid for field lookups but valid
- * for the element level lookups. I should rather not create the
- * FieldElements this way.
- || (
- elm->getNode( dataIndex ) == Shell::myNode() &&
- fieldIndex >= elm->numField( dataIndex - elm->localDataStart() )
- )
- */
- );
+ Element* elm = id.element();
+ return ( elm == 0 ||
+ dataIndex == BADINDEX ||
+ fieldIndex == BADINDEX ||
+ dataIndex >= elm->numData()
+ /*
+ * We have a bit of a problem here. The FieldElement can exist
+ * with zero fields, and is invalid for field lookups but valid
+ * for the element level lookups. I should rather not create the
+ * FieldElements this way.
+ || (
+ elm->getNode( dataIndex ) == Shell::myNode() &&
+ fieldIndex >= elm->numField( dataIndex - elm->localDataStart() )
+ )
+ */
+ );
}
ostream& operator <<( ostream& s, const ObjId& i )
{
- if ( i.dataIndex == 0 && i.fieldIndex == 0 )
- s << i.id;
- else if ( i.fieldIndex == 0 )
- s << i.id << "[" << i.dataIndex << "]";
- else
- s << i.id << "[" << i.dataIndex << "][" << i.fieldIndex << "]";
- return s;
+ if ( i.dataIndex == 0 && i.fieldIndex == 0 )
+ s << i.id;
+ else if ( i.fieldIndex == 0 )
+ s << i.id << "[" << i.dataIndex << "]";
+ else
+ s << i.id << "[" << i.dataIndex << "][" << i.fieldIndex << "]";
+ return s;
}
/**
@@ -51,77 +51,77 @@ ostream& operator <<( ostream& s, const ObjId& i )
*/
istream& operator >>( istream& s, ObjId& i )
{
- s >> i.id;
- return s;
+ s >> i.id;
+ return s;
}
//////////////////////////////////////////////////////////////
ObjId::ObjId( const string& path )
{
- Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
- assert( shell );
- *this = shell->doFind( path );
+ Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
+ assert( shell );
+ *this = shell->doFind( path );
}
Eref ObjId::eref() const
{
- return Eref( id.element(), dataIndex, fieldIndex );
+ return Eref( id.element(), dataIndex, fieldIndex );
}
bool ObjId::operator==( const ObjId& other ) const
{
- return ( id == other.id && dataIndex == other.dataIndex &&
- fieldIndex == other.fieldIndex );
+ return ( id == other.id && dataIndex == other.dataIndex &&
+ fieldIndex == other.fieldIndex );
}
bool ObjId::operator!=( const ObjId& other ) const
{
- return ( id != other.id || dataIndex != other.dataIndex ||
- fieldIndex != other.fieldIndex );
+ return ( id != other.id || dataIndex != other.dataIndex ||
+ fieldIndex != other.fieldIndex );
}
bool ObjId::operator<( const ObjId& other ) const
{
- return ( id < other.id ||
- (id == other.id && (
- dataIndex < other.dataIndex ||
- ( dataIndex == other.dataIndex &&
- fieldIndex < other.fieldIndex )
- )
- )
- );
+ return ( id < other.id ||
+ (id == other.id && (
+ dataIndex < other.dataIndex ||
+ ( dataIndex == other.dataIndex &&
+ fieldIndex < other.fieldIndex )
+ )
+ )
+ );
}
bool ObjId::isDataHere() const
{
- return ( id.element()->getNode( dataIndex ) == Shell::myNode() );
+ return ( id.element()->getNode( dataIndex ) == Shell::myNode() );
}
bool ObjId::isGlobal() const
{
- return ( id.element()->isGlobal() );
+ return ( id.element()->isGlobal() );
}
bool ObjId::isOffNode() const
{
- return ( Shell::numNodes() > 1 &&
- ( id.element()->isGlobal() ||
- id.element()->getNode( dataIndex ) != Shell::myNode() )
- );
+ return ( Shell::numNodes() > 1 &&
+ ( id.element()->isGlobal() ||
+ id.element()->getNode( dataIndex ) != Shell::myNode() )
+ );
}
char* ObjId::data() const
{
- return id.element()->data( id.element()->rawIndex( dataIndex ),
- fieldIndex );
+ return id.element()->data( id.element()->rawIndex( dataIndex ),
+ fieldIndex );
}
string ObjId::path() const
{
- return Neutral::path( eref() );
+ return Neutral::path( eref() );
}
Element* ObjId::element() const
{
- return id.element();
+ return id.element();
}
diff --git a/moose-core/basecode/ObjId.h b/moose-core/basecode/ObjId.h
index 9f279f453fe2619698501642075dae85aa90a938..ab91204c2360c356f657d3fc99388d721a65b159 100644
--- a/moose-core/basecode/ObjId.h
+++ b/moose-core/basecode/ObjId.h
@@ -19,95 +19,102 @@
*/
class ObjId
{
- friend ostream& operator <<( ostream& s, const ObjId& i );
- friend istream& operator >>( istream& s, ObjId& i );
- public:
- //////////////////////////////////////////////////////////////
- // ObjId creation
- //////////////////////////////////////////////////////////////
- /**
- * Returns the root Id
- */
- ObjId()
- : id(), dataIndex( 0 ), fieldIndex( 0 )
- {;}
-
- /**
- * Creates a ObjId using specified Id and DataIndex
- */
- ObjId( Id i, unsigned int d, unsigned int f = 0 )
- : id( i ), dataIndex( d ), fieldIndex( f )
- {;}
-
- ObjId( Id i )
- : id( i ), dataIndex( 0 ), fieldIndex( 0 )
- {;}
-
- /**
- * Creates an ObjId by reading the path string
- * Returns bad on failure.
- */
- ObjId( const string& path );
-
- /**
- * Returns the absolute path including all array indices.
- */
- string path() const;
-
- /**
- * Returns the Eref matching itself.
- */
- Eref eref() const;
-
- /**
- * For equality check
- */
- bool operator==( const ObjId& other ) const;
- bool operator!=( const ObjId& other ) const;
-
- /**
- * For sorting
- */
- bool operator<( const ObjId& other ) const;
-
- /**
- * True if the data is present on the current node. Always true for
- * globals, which confuses the matter somewhat.
- */
- bool isDataHere() const;
-
- /// Returns true if the Element is global.
- bool isGlobal() const;
-
- /// Returns true if we need to go off-node for calling operations
- bool isOffNode() const;
-
- /**
- * Returns data entry for this object
- */
- char* data() const;
-
- /**
- * Returns Element part
- */
- Element* element() const;
-
- /**
- * Here are the data values.
- */
- Id id;
- unsigned int dataIndex;
- unsigned int fieldIndex;
-
- /**
- * True if the return value is bad: either returning a failure,
- * or the DataIndex or FieldIndex is out of range. However, this
- * is a node-local funtion so it can't report the FieldIndex status
- * in all cases.
- */
- bool bad() const;
-
- private:
+ friend ostream& operator <<( ostream& s, const ObjId& i );
+ friend istream& operator >>( istream& s, ObjId& i );
+
+public:
+ //////////////////////////////////////////////////////////////
+ // ObjId creation
+ //////////////////////////////////////////////////////////////
+ /**
+ * Returns the root Id
+ */
+ ObjId()
+ : id(), dataIndex( 0 ), fieldIndex( 0 )
+ {
+ ;
+ }
+
+ /**
+ * Creates a ObjId using specified Id and DataIndex
+ */
+ ObjId( Id i, unsigned int d, unsigned int f = 0 )
+ : id( i ), dataIndex( d ), fieldIndex( f )
+ {
+ ;
+ }
+
+ ObjId( Id i )
+ : id( i ), dataIndex( 0 ), fieldIndex( 0 )
+ {
+ ;
+ }
+
+ /**
+ * Creates an ObjId by reading the path string
+ * Returns bad on failure.
+ */
+ ObjId( const string& path );
+
+ /**
+ * Returns the absolute path including all array indices.
+ */
+ string path() const;
+
+ /**
+ * Returns the Eref matching itself.
+ */
+ Eref eref() const;
+
+ /**
+ * For equality check
+ */
+ bool operator==( const ObjId& other ) const;
+ bool operator!=( const ObjId& other ) const;
+
+ /**
+ * For sorting
+ */
+ bool operator<( const ObjId& other ) const;
+
+ /**
+ * True if the data is present on the current node. Always true for
+ * globals, which confuses the matter somewhat.
+ */
+ bool isDataHere() const;
+
+ /// Returns true if the Element is global.
+ bool isGlobal() const;
+
+ /// Returns true if we need to go off-node for calling operations
+ bool isOffNode() const;
+
+ /**
+ * Returns data entry for this object
+ */
+ char* data() const;
+
+ /**
+ * Returns Element part
+ */
+ Element* element() const;
+
+ /**
+ * Here are the data values.
+ */
+ Id id;
+ unsigned int dataIndex;
+ unsigned int fieldIndex;
+
+ /**
+ * True if the return value is bad: either returning a failure,
+ * or the DataIndex or FieldIndex is out of range. However, this
+ * is a node-local funtion so it can't report the FieldIndex status
+ * in all cases.
+ */
+ bool bad() const;
+
+private:
};
#endif // _OBJ_ID_H
diff --git a/moose-core/basecode/SetGet.h b/moose-core/basecode/SetGet.h
index fc855b2071b4c123c631be6fcc9786e051b6b5dd..1788d6addae20084dac985df22bf999304fd506c 100644
--- a/moose-core/basecode/SetGet.h
+++ b/moose-core/basecode/SetGet.h
@@ -29,325 +29,350 @@ template< class T, class A > class GetOpFunc;
template< class T, class A >
A localGet( const Eref& er, string field )
{
- string fullFieldName = "get" + field;
- fullFieldName[3] = std::toupper( fullFieldName[3] );
- const Finfo* finfo = er.element()->cinfo()->findFinfo( fullFieldName );
- assert( finfo );
+ string fullFieldName = "get" + field;
+ fullFieldName[3] = std::toupper( fullFieldName[3] );
+ const Finfo* finfo = er.element()->cinfo()->findFinfo( fullFieldName );
+ assert( finfo );
- const DestFinfo* dest = dynamic_cast< const DestFinfo* >( finfo );
- assert( dest );
+ const DestFinfo* dest = dynamic_cast< const DestFinfo* >( finfo );
+ assert( dest );
- const OpFunc* op = dest->getOpFunc();
- assert( op );
+ const OpFunc* op = dest->getOpFunc();
+ assert( op );
- const GetOpFunc< T, A >* gop =
- dynamic_cast< const GetOpFunc< T, A >* >( op );
- assert( gop );
+ const GetOpFunc< T, A >* gop =
+ dynamic_cast< const GetOpFunc< T, A >* >( op );
+ assert( gop );
- return gop->reduceOp( er );
+ return gop->reduceOp( er );
}
class SetGet
{
- public:
- SetGet()
- {;}
-
- virtual ~SetGet()
- {;}
-
- /**
- * Utility function to check that the target field matches this
- * source type, to look up and pass back the fid, and to return
- * the number of targetEntries.
- * Tgt is passed in as the destination ObjId. May be changed inside,
- * if the function determines that it should be directed to a
- * child Element acting as a Value.
- * Checks arg # and types for a 'set' call. Can be zero to 3 args.
- * Returns # of tgts if good. This is 0 if bad.
- * Passes back found fid.
- */
- static const OpFunc* checkSet(
- const string& field, ObjId& tgt, FuncId& fid );
+public:
+ SetGet()
+ {
+ ;
+ }
+
+ virtual ~SetGet()
+ {
+ ;
+ }
+
+ /**
+ * Utility function to check that the target field matches this
+ * source type, to look up and pass back the fid, and to return
+ * the number of targetEntries.
+ * Tgt is passed in as the destination ObjId. May be changed inside,
+ * if the function determines that it should be directed to a
+ * child Element acting as a Value.
+ * Checks arg # and types for a 'set' call. Can be zero to 3 args.
+ * Returns # of tgts if good. This is 0 if bad.
+ * Passes back found fid.
+ */
+ static const OpFunc* checkSet(
+ const string& field, ObjId& tgt, FuncId& fid );
//////////////////////////////////////////////////////////////////////
- /**
- * Blocking 'get' call, returning into a string.
- * There is a matching 'get<T> call, returning appropriate type.
- */
- static bool strGet( const ObjId& tgt, const string& field, string& ret );
-
- /**
- * Blocking 'set' call, using automatic string conversion
- * There is a matching blocking set call with typed arguments.
- */
- static bool strSet( const ObjId& dest, const string& field, const string& val );
-
- /// Sends out request for data, and awaits its return.
- static const vector< double* >* dispatchGet(
- const ObjId& tgt, FuncId tgtFid,
- const double* arg, unsigned int size );
-
- virtual bool checkOpClass( const OpFunc* op ) const = 0;
+ /**
+ * Blocking 'get' call, returning into a string.
+ * There is a matching 'get<T> call, returning appropriate type.
+ */
+ static bool strGet( const ObjId& tgt, const string& field, string& ret );
+
+ /**
+ * Blocking 'set' call, using automatic string conversion
+ * There is a matching blocking set call with typed arguments.
+ */
+ static bool strSet( const ObjId& dest, const string& field, const string& val );
+
+ /// Sends out request for data, and awaits its return.
+ static const vector< double* >* dispatchGet(
+ const ObjId& tgt, FuncId tgtFid,
+ const double* arg, unsigned int size );
+
+ virtual bool checkOpClass( const OpFunc* op ) const = 0;
};
class SetGet0: public SetGet
{
- public:
- SetGet0()
- {;}
-
- /**
- * Blocking, typed 'Set' call
- */
- static bool set( const ObjId& dest, const string& field )
- {
- FuncId fid;
- ObjId tgt( dest ); // checkSet may change the tgt.
- const OpFunc* func = checkSet( field, tgt, fid );
- const OpFunc0Base* op =
- dynamic_cast< const OpFunc0Base* >( func );
- if ( op ) {
- if ( tgt.isOffNode() ) {
- const OpFunc* op2 = op->makeHopFunc(
- HopIndex( op->opIndex(), MooseSetHop ) );
- const OpFunc0Base* hop =
- dynamic_cast< const OpFunc0Base* >( op2 );
- assert( hop );
- hop->op( tgt.eref() );
- delete op2;
- if ( tgt.isGlobal() )
- op->op( tgt.eref() );
- return true;
- } else {
- op->op( tgt.eref() );
- return true;
- }
- }
- return 0;
- }
-
- /**
- * Blocking call using string conversion
- */
- static bool innerStrSet( const ObjId& dest, const string& field,
- const string& val )
- {
- return set( dest, field );
- }
-
- bool checkOpClass( const OpFunc* op ) const {
- return dynamic_cast< const OpFunc0Base* >( op );
- }
+public:
+ SetGet0()
+ {
+ ;
+ }
+
+ /**
+ * Blocking, typed 'Set' call
+ */
+ static bool set( const ObjId& dest, const string& field )
+ {
+ FuncId fid;
+ ObjId tgt( dest ); // checkSet may change the tgt.
+ const OpFunc* func = checkSet( field, tgt, fid );
+ const OpFunc0Base* op =
+ dynamic_cast< const OpFunc0Base* >( func );
+ if ( op )
+ {
+ if ( tgt.isOffNode() )
+ {
+ const OpFunc* op2 = op->makeHopFunc(
+ HopIndex( op->opIndex(), MooseSetHop ) );
+ const OpFunc0Base* hop =
+ dynamic_cast< const OpFunc0Base* >( op2 );
+ assert( hop );
+ hop->op( tgt.eref() );
+ delete op2;
+ if ( tgt.isGlobal() )
+ op->op( tgt.eref() );
+ return true;
+ }
+ else
+ {
+ op->op( tgt.eref() );
+ return true;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Blocking call using string conversion
+ */
+ static bool innerStrSet( const ObjId& dest, const string& field,
+ const string& val )
+ {
+ return set( dest, field );
+ }
+
+ bool checkOpClass( const OpFunc* op ) const
+ {
+ return dynamic_cast< const OpFunc0Base* >( op );
+ }
};
template< class A > class SetGet1: public SetGet
{
- public:
- SetGet1()
- {;}
-
- /**
- * Blocking, typed 'Set' call
- */
- static bool set( const ObjId& dest, const string& field, A arg )
- {
- FuncId fid;
- ObjId tgt( dest );
- const OpFunc* func = checkSet( field, tgt, fid );
- const OpFunc1Base< A >* op =
- dynamic_cast< const OpFunc1Base< A >* >( func );
- if ( op ) {
- if ( tgt.isOffNode() ) {
- const OpFunc* op2 = op->makeHopFunc(
- HopIndex( op->opIndex(), MooseSetHop ) );
- const OpFunc1Base< A >* hop =
- dynamic_cast< const OpFunc1Base< A >* >( op2 );
- hop->op( tgt.eref(), arg );
- delete op2;
- if ( tgt.isGlobal() )
- op->op( tgt.eref(), arg );
- return true;
- } else {
- op->op( tgt.eref(), arg );
- return true;
- }
- }
- return false;
- }
-
- /**
- * setVec assigns all the entries in the target Id to the
- * specified vector of values. If the target is a FieldElement
- * it assigns the entries on the specific DataIndex provided in the
- * ObjId argument.
- * The vector is used as a circular
- * buffer: if the number of targets exceeds the vector size, it
- * rolls over.
- */
- static bool setVec( ObjId destId, const string& field,
- const vector< A >& arg )
- {
- if ( arg.size() == 0 ) return 0;
-
- ObjId tgt( destId );
- FuncId fid;
-
- const OpFunc* func = checkSet( field, tgt, fid );
- const OpFunc1Base< A >* op = dynamic_cast< const OpFunc1Base< A >* >( func );
- if ( op ) {
- const OpFunc* op2 = op->makeHopFunc(
- HopIndex( op->opIndex(), MooseSetVecHop ) );
- const OpFunc1Base< A >* hop =
- dynamic_cast< const OpFunc1Base< A >* >( op2 );
- hop->opVec( tgt.eref(), arg, op );
- delete op2;
- return true;
- }
- return false;
- }
-
- /**
- * Sets all target array values to the single value
- */
- static bool setRepeat( ObjId destId, const string& field,
- const A& arg )
- {
- vector< A >temp ( 1, arg );
- return setVec( destId, field, temp );
- }
-
- /**
- * Blocking call using string conversion
- */
- static bool innerStrSet( const ObjId& dest, const string& field,
- const string& val )
- {
- A arg;
- Conv< A >::str2val( arg, val );
- return set( dest, field, arg );
- }
-
- bool checkOpClass( const OpFunc* op ) const {
- return dynamic_cast< const OpFunc1Base< A > * >( op );
- }
+public:
+ SetGet1()
+ {
+ ;
+ }
+
+ /**
+ * Blocking, typed 'Set' call
+ */
+ static bool set( const ObjId& dest, const string& field, A arg )
+ {
+ FuncId fid;
+ ObjId tgt( dest );
+ const OpFunc* func = checkSet( field, tgt, fid );
+ const OpFunc1Base< A >* op = dynamic_cast< const OpFunc1Base< A >* >( func );
+ if ( op )
+ {
+ if ( tgt.isOffNode() )
+ {
+ const OpFunc* op2 = op->makeHopFunc(
+ HopIndex( op->opIndex(), MooseSetHop ) );
+ const OpFunc1Base< A >* hop =
+ dynamic_cast< const OpFunc1Base< A >* >( op2 );
+ hop->op( tgt.eref(), arg );
+ delete op2;
+ if ( tgt.isGlobal() )
+ op->op( tgt.eref(), arg );
+ return true;
+ }
+ else
+ {
+ op->op( tgt.eref(), arg );
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * setVec assigns all the entries in the target Id to the
+ * specified vector of values. If the target is a FieldElement
+ * it assigns the entries on the specific DataIndex provided in the
+ * ObjId argument.
+ * The vector is used as a circular
+ * buffer: if the number of targets exceeds the vector size, it
+ * rolls over.
+ */
+ static bool setVec( ObjId destId, const string& field,
+ const vector< A >& arg )
+ {
+ if ( arg.size() == 0 ) return 0;
+
+ ObjId tgt( destId );
+ FuncId fid;
+
+ const OpFunc* func = checkSet( field, tgt, fid );
+ const OpFunc1Base< A >* op = dynamic_cast< const OpFunc1Base< A >* >( func );
+ if ( op )
+ {
+ const OpFunc* op2 = op->makeHopFunc(
+ HopIndex( op->opIndex(), MooseSetVecHop ) );
+ const OpFunc1Base< A >* hop =
+ dynamic_cast< const OpFunc1Base< A >* >( op2 );
+ hop->opVec( tgt.eref(), arg, op );
+ delete op2;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Sets all target array values to the single value
+ */
+ static bool setRepeat( ObjId destId, const string& field,
+ const A& arg )
+ {
+ vector< A >temp ( 1, arg );
+ return setVec( destId, field, temp );
+ }
+
+ /**
+ * Blocking call using string conversion
+ */
+ static bool innerStrSet( const ObjId& dest, const string& field,
+ const string& val )
+ {
+ A arg;
+ Conv< A >::str2val( arg, val );
+ return set( dest, field, arg );
+ }
+
+ bool checkOpClass( const OpFunc* op ) const
+ {
+ return dynamic_cast< const OpFunc1Base< A > * >( op );
+ }
};
template< class A > class Field: public SetGet1< A >
{
- public:
- Field()
- {;}
-
- /**
- * Blocking, typed 'Set' call
- */
- static bool set( const ObjId& dest, const string& field, A arg )
- {
- string temp = "set" + field;
- temp[3] = std::toupper( temp[3] );
- return SetGet1< A >::set( dest, temp, arg );
- }
-
- static bool setVec( ObjId destId, const string& field,
- const vector< A >& arg )
- {
- string temp = "set" + field;
- temp[3] = std::toupper( temp[3] );
- return SetGet1< A >::setVec( destId, temp, arg );
- }
-
- static bool setRepeat( ObjId destId, const string& field,
- A arg )
- {
- string temp = "set" + field;
- temp[3] = std::toupper( temp[3] );
- return SetGet1< A >::setRepeat( destId, temp, arg );
- }
-
- /**
- * Blocking call using string conversion
- */
- static bool innerStrSet( const ObjId& dest, const string& field,
- const string& arg )
- {
- A val;
- // Do NOT add 'set_' to the field name, as the 'set' func
- // does it anyway.
- Conv< A >::str2val( val, arg );
- return set( dest, field, val );
- }
-
- //////////////////////////////////////////////////////////////////
-
- // Returns a field value.
- static A get( const ObjId& dest, const string& field)
- {
- ObjId tgt( dest );
- FuncId fid;
- string fullFieldName = "get" + field;
- fullFieldName[3] = std::toupper( fullFieldName[3] );
- const OpFunc* func = SetGet::checkSet( fullFieldName, tgt, fid );
- const GetOpFuncBase< A >* gof =
- dynamic_cast< const GetOpFuncBase< A >* >( func );
- if ( gof ) {
- if ( tgt.isDataHere() ) {
- return gof->returnOp( tgt.eref() );
- } else {
- const OpFunc* op2 = gof->makeHopFunc(
- HopIndex( gof->opIndex(), MooseGetHop ) );
- const OpFunc1Base< A* >* hop =
- dynamic_cast< const OpFunc1Base< A* >* >( op2 );
- assert( hop );
- // Blocking function.
- A ret;
- hop->op( tgt.eref(), &ret );
- delete op2;
- return ret;
- }
- }
- cout << "Warning: Field::Get conversion error for " <<
- dest.id.path() << "." << field << endl;
- return A();
- }
-
- /**
- * Returns a vector of values
- */
- static void getVec( ObjId dest, const string& field, vector< A >& vec)
- {
-
- vec.resize( 0 );
- ObjId tgt( dest );
- FuncId fid;
- string fullFieldName = "get" + field;
- fullFieldName[3] = std::toupper( fullFieldName[3] );
- const OpFunc* func = SetGet::checkSet( fullFieldName, tgt, fid );
- const GetOpFuncBase< A >* gof =
- dynamic_cast< const GetOpFuncBase< A >* >( func );
- if ( gof ) {
- const OpFunc* op2 = gof->makeHopFunc(
- HopIndex( gof->opIndex(), MooseGetVecHop ) );
- const GetHopFunc< A >* hop =
- dynamic_cast< const GetHopFunc< A >* >( op2 );
- hop->opGetVec( tgt.eref(), vec, gof );
- delete op2;
- return;
- }
- cout << "Warning: Field::getVec conversion error for " <<
- dest.path() << endl;
- }
-
- /**
- * Blocking call for finding a value and returning in a
- * string.
- */
- static bool innerStrGet( const ObjId& dest, const string& field,
- string& str )
- {
- Conv< A >::val2str( str, get( dest, field ) );
- return 1;
- }
+public:
+ Field()
+ {
+ ;
+ }
+
+ /**
+ * Blocking, typed 'Set' call
+ */
+ static bool set( const ObjId& dest, const string& field, A arg )
+ {
+ string temp = "set" + field;
+ temp[3] = std::toupper( temp[3] );
+ return SetGet1< A >::set( dest, temp, arg );
+ }
+
+ static bool setVec( ObjId destId, const string& field,
+ const vector< A >& arg )
+ {
+ string temp = "set" + field;
+ temp[3] = std::toupper( temp[3] );
+ return SetGet1< A >::setVec( destId, temp, arg );
+ }
+
+ static bool setRepeat( ObjId destId, const string& field,
+ A arg )
+ {
+ string temp = "set" + field;
+ temp[3] = std::toupper( temp[3] );
+ return SetGet1< A >::setRepeat( destId, temp, arg );
+ }
+
+ /**
+ * Blocking call using string conversion
+ */
+ static bool innerStrSet( const ObjId& dest, const string& field,
+ const string& arg )
+ {
+ A val;
+ // Do NOT add 'set_' to the field name, as the 'set' func
+ // does it anyway.
+ Conv< A >::str2val( val, arg );
+ return set( dest, field, val );
+ }
+
+ //////////////////////////////////////////////////////////////////
+
+ // Returns a field value.
+ static A get( const ObjId& dest, const string& field)
+ {
+ ObjId tgt( dest );
+ FuncId fid;
+ string fullFieldName = "get" + field;
+ fullFieldName[3] = std::toupper( fullFieldName[3] );
+ const OpFunc* func = SetGet::checkSet( fullFieldName, tgt, fid );
+ const GetOpFuncBase< A >* gof =
+ dynamic_cast< const GetOpFuncBase< A >* >( func );
+ if ( gof )
+ {
+ if ( tgt.isDataHere() )
+ {
+ return gof->returnOp( tgt.eref() );
+ }
+ else
+ {
+ const OpFunc* op2 = gof->makeHopFunc(
+ HopIndex( gof->opIndex(), MooseGetHop ) );
+ const OpFunc1Base< A* >* hop =
+ dynamic_cast< const OpFunc1Base< A* >* >( op2 );
+ assert( hop );
+ // Blocking function.
+ A ret;
+ hop->op( tgt.eref(), &ret );
+ delete op2;
+ return ret;
+ }
+ }
+ cout << "Warning: Field::Get conversion error for " <<
+ dest.id.path() << "." << field << endl;
+ return A();
+ }
+
+ /**
+ * Returns a vector of values
+ */
+ static void getVec( ObjId dest, const string& field, vector< A >& vec)
+ {
+
+ vec.resize( 0 );
+ ObjId tgt( dest );
+ FuncId fid;
+ string fullFieldName = "get" + field;
+ fullFieldName[3] = std::toupper( fullFieldName[3] );
+ const OpFunc* func = SetGet::checkSet( fullFieldName, tgt, fid );
+ const GetOpFuncBase< A >* gof =
+ dynamic_cast< const GetOpFuncBase< A >* >( func );
+ if ( gof )
+ {
+ const OpFunc* op2 = gof->makeHopFunc(
+ HopIndex( gof->opIndex(), MooseGetVecHop ) );
+ const GetHopFunc< A >* hop =
+ dynamic_cast< const GetHopFunc< A >* >( op2 );
+ hop->opGetVec( tgt.eref(), vec, gof );
+ delete op2;
+ return;
+ }
+ cout << "Warning: Field::getVec conversion error for " <<
+ dest.path() << endl;
+ }
+
+ /**
+ * Blocking call for finding a value and returning in a
+ * string.
+ */
+ static bool innerStrGet( const ObjId& dest, const string& field,
+ string& str )
+ {
+ Conv< A >::val2str( str, get( dest, field ) );
+ return 1;
+ }
};
/**
@@ -355,95 +380,102 @@ template< class A > class Field: public SetGet1< A >
*/
template< class A1, class A2 > class SetGet2: public SetGet
{
- public:
- SetGet2()
- {;}
-
- /**
- * Blocking, typed 'Set' call
- */
- static bool set( const ObjId& dest, const string& field,
- A1 arg1, A2 arg2 )
- {
- FuncId fid;
- ObjId tgt( dest );
- const OpFunc* func = checkSet( field, tgt, fid );
- const OpFunc2Base< A1, A2 >* op =
- dynamic_cast< const OpFunc2Base< A1, A2 >* >( func );
- if ( op ) {
- if ( tgt.isOffNode() ) {
- const OpFunc* op2 = op->makeHopFunc(
- HopIndex( op->opIndex(), MooseSetHop ) );
- const OpFunc2Base< A1, A2 >* hop =
- dynamic_cast< const OpFunc2Base< A1, A2 >* >( op2 );
- hop->op( tgt.eref(), arg1, arg2 );
- delete op2;
- if ( tgt.isGlobal() )
- op->op( tgt.eref(), arg1, arg2 );
- return true;
- } else {
- op->op( tgt.eref(), arg1, arg2 );
- return true;
- }
- }
- return false;
- }
-
- /**
- * Assign a vector of targets, using matching vectors of arguments
- * arg1 and arg2. Specifically, index i on the target receives
- * arguments arg1[i], arg2[i].
- * Note that there is no requirement for the size of the
- * argument vectors to be equal to the size of the target array
- * of objects. If there are fewer arguments then the index cycles
- * back, so as to tile the target array with as many arguments as
- * we have.
- *
- * Not yet implemented correct handling for FieldElements.
- */
- static bool setVec( Id destId, const string& field,
- const vector< A1 >& arg1, const vector< A2 >& arg2 )
- {
- ObjId tgt( destId, 0 );
- FuncId fid;
- const OpFunc* func = checkSet( field, tgt, fid );
- const OpFunc2Base< A1, A2 >* op =
- dynamic_cast< const OpFunc2Base< A1, A2 >* >( func );
- if ( op ) {
- /*
- unsigned int size = tgt.element()->numData();
- // total # of entries on element and maybe to include fields
- for ( unsigned int i = 0; i < size; ++i ) {
- Eref er( tgt.element(), i );
- op->op( er, arg1[ i % arg1.size() ],
- arg2[ i % arg2.size() ] );
- }
- return true;
- */
- const OpFunc* op2 = op->makeHopFunc(
- HopIndex( op->opIndex(), MooseSetVecHop ) );
- const OpFunc2Base< A1, A2 >* hop =
- dynamic_cast< const OpFunc2Base< A1, A2 >* >( op2 );
- hop->opVec( tgt.eref(), arg1, arg2, op );
- delete op2;
- return true;
- }
- return false;
- }
-
- /**
- * Blocking call using string conversion.
- */
- static bool innerStrSet( const ObjId& dest, const string& field,
- const string& val )
- {
- A1 arg1;
- A2 arg2;
- string::size_type pos = val.find_first_of( "," );
- Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
- Conv< A2 >::str2val( arg2, val.substr( pos + 1 ) );
- return set( dest, field, arg1, arg2 );
- }
+public:
+ SetGet2()
+ {
+ ;
+ }
+
+ /**
+ * Blocking, typed 'Set' call
+ */
+ static bool set( const ObjId& dest, const string& field,
+ A1 arg1, A2 arg2 )
+ {
+ FuncId fid;
+ ObjId tgt( dest );
+ const OpFunc* func = checkSet( field, tgt, fid );
+ const OpFunc2Base< A1, A2 >* op =
+ dynamic_cast< const OpFunc2Base< A1, A2 >* >( func );
+ if ( op )
+ {
+ if ( tgt.isOffNode() )
+ {
+ const OpFunc* op2 = op->makeHopFunc(
+ HopIndex( op->opIndex(), MooseSetHop ) );
+ const OpFunc2Base< A1, A2 >* hop =
+ dynamic_cast< const OpFunc2Base< A1, A2 >* >( op2 );
+ hop->op( tgt.eref(), arg1, arg2 );
+ delete op2;
+ if ( tgt.isGlobal() )
+ op->op( tgt.eref(), arg1, arg2 );
+ return true;
+ }
+ else
+ {
+ op->op( tgt.eref(), arg1, arg2 );
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Assign a vector of targets, using matching vectors of arguments
+ * arg1 and arg2. Specifically, index i on the target receives
+ * arguments arg1[i], arg2[i].
+ * Note that there is no requirement for the size of the
+ * argument vectors to be equal to the size of the target array
+ * of objects. If there are fewer arguments then the index cycles
+ * back, so as to tile the target array with as many arguments as
+ * we have.
+ *
+ * Not yet implemented correct handling for FieldElements.
+ */
+ static bool setVec( Id destId, const string& field,
+ const vector< A1 >& arg1, const vector< A2 >& arg2 )
+ {
+ ObjId tgt( destId, 0 );
+ FuncId fid;
+ const OpFunc* func = checkSet( field, tgt, fid );
+ const OpFunc2Base< A1, A2 >* op =
+ dynamic_cast< const OpFunc2Base< A1, A2 >* >( func );
+ if ( op )
+ {
+ /*
+ unsigned int size = tgt.element()->numData();
+ // total # of entries on element and maybe to include fields
+ for ( unsigned int i = 0; i < size; ++i ) {
+ Eref er( tgt.element(), i );
+ op->op( er, arg1[ i % arg1.size() ],
+ arg2[ i % arg2.size() ] );
+ }
+ return true;
+ */
+ const OpFunc* op2 = op->makeHopFunc(
+ HopIndex( op->opIndex(), MooseSetVecHop ) );
+ const OpFunc2Base< A1, A2 >* hop =
+ dynamic_cast< const OpFunc2Base< A1, A2 >* >( op2 );
+ hop->opVec( tgt.eref(), arg1, arg2, op );
+ delete op2;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Blocking call using string conversion.
+ */
+ static bool innerStrSet( const ObjId& dest, const string& field,
+ const string& val )
+ {
+ A1 arg1;
+ A2 arg2;
+ string::size_type pos = val.find_first_of( "," );
+ Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
+ Conv< A2 >::str2val( arg2, val.substr( pos + 1 ) );
+ return set( dest, field, arg1, arg2 );
+ }
};
/**
@@ -456,159 +488,167 @@ template< class A1, class A2 > class SetGet2: public SetGet
*/
template< class L, class A > class LookupField: public SetGet2< L, A >
{
- public:
- LookupField( const ObjId& dest )
- : SetGet2< L, A >( dest )
- {;}
-
- /**
- * Blocking, typed 'Set' call. Identical to SetGet2::set.
- */
- static bool set( const ObjId& dest, const string& field,
- L index, A arg )
- {
- string temp = "set" + field;
- temp[3] = std::toupper( temp[3] );
- return SetGet2< L, A >::set( dest, temp, index, arg );
- }
-
- /**
- * This setVec assigns goes through each object entry in the
- * destId, and assigns the corresponding index and argument to it.
- */
- static bool setVec( Id destId, const string& field,
- const vector< L >& index, const vector< A >& arg )
- {
- string temp = "set" + field;
- temp[3] = std::toupper( temp[3] );
- return SetGet2< L, A >::setVec( destId, temp, index, arg );
- }
-
- /**
- * This setVec takes a specific object entry, presumably one with
- * an array of values within it. The it goes through each specified
- * index and assigns the corresponding argument.
- * This is a brute-force assignment.
- */
- static bool setVec( ObjId dest, const string& field,
- const vector< L >& index, const vector< A >& arg )
- {
- string temp = "set" + field;
- temp[3] = std::toupper( temp[3] );
- return SetGet2< L, A >::setVec( dest, temp, index, arg );
- }
-
- /**
- * Faking setRepeat too. Just plugs into setVec.
- */
- static bool setRepeat( Id destId, const string& field,
- const vector< L >& index, A arg )
- {
- vector< A > avec( index.size(), arg );
- return setVec( destId, field, index, avec );
- }
-
- /**
- * Blocking call using string conversion
- */
- static bool innerStrSet( const ObjId& dest, const string& field,
- const string& indexStr, const string& val )
- {
- L index;
- Conv< L >::str2val( index, indexStr );
-
- A arg;
- // Do NOT add 'set_' to the field name, as the 'set' func
- // does it anyway.
- Conv< A >::str2val( arg, val );
- return set( dest, field, index, arg );
- }
-
- /**
- * Gets a value on a specific object, looking it up using the
- * provided index.
- */
- // Returns a field value.
- static A get( const ObjId& dest, const string& field, L index )
- {
- ObjId tgt( dest );
- FuncId fid;
- string fullFieldName = "get" + field;
- fullFieldName[3] = std::toupper( fullFieldName[3] );
- const OpFunc* func = SetGet::checkSet( fullFieldName, tgt, fid);
- const LookupGetOpFuncBase< L, A >* gof =
- dynamic_cast< const LookupGetOpFuncBase< L, A >* >( func );
- if ( gof ) {
- if ( tgt.isDataHere() ) {
- return gof->returnOp( tgt.eref(), index );
- } else {
- /*
- const OpFunc* op2 = gof->makeHopFunc(
- HopIndex( gof->opIndex(), MooseGetHop ), index );
- const OpFunc1Base< A* >* hop =
- dynamic_cast< const OpFunc1Base< A* >* >( op2 );
- */
- cout << "Warning: LookupField::get: cannot cross nodes yet\n";
- return A();
- /*
- assert( hop );
- // Blocking function.
- hop->op( tgt.eref(), &ret );
- delete op2;
- return ret;
- */
- }
- }
- cout << "LookupField::get: Warning: Field::Get conversion error for " <<
- dest.id.path() << "." << field << endl;
- return A();
- }
-
- /**
- * Blocking call that returns a vector of values in vec.
- * This variant goes through each target object entry on dest,
- * and passes in the same lookup index to each one. The results
- * are put together in the vector vec.
- */
- static void getVec( Id dest, const string& field,
- vector< L >& index, vector< A >& vec )
- {
- vec.resize( 0 );
- ObjId tgt( dest );
- FuncId fid;
- string fullFieldName = "get" + field;
- fullFieldName[3] = std::toupper( fullFieldName[3] );
- const OpFunc* func = SetGet::checkSet( fullFieldName, tgt, fid );
- const LookupGetOpFuncBase< L, A >* gof =
- dynamic_cast< const LookupGetOpFuncBase< L, A >* >( func );
- if ( gof ) {
- Element* elm = dest.element();
- unsigned int size = vec.size(); // temporary. See SetVec.
- vec.resize( size );
- for ( unsigned int i = 0; i < size; ++i ) {
- Eref e( elm, i );
- vec[i] = gof->returnOp( e, index );
- }
- return;
- }
- cout << "Warning: Field::getVec conversion error for " <<
- dest.path() << endl;
- }
-
- /**
- * Blocking virtual call for finding a value and returning in a
- * string.
- */
- static bool innerStrGet( const ObjId& dest, const string& field,
- const string& indexStr, string& str )
- {
- L index;
- Conv< L >::str2val( index, indexStr );
-
- A ret = get( dest, field, index );
- Conv<A>::val2str( str, ret );
- return 1;
- }
+public:
+ LookupField( const ObjId& dest )
+ : SetGet2< L, A >( dest )
+ {
+ ;
+ }
+
+ /**
+ * Blocking, typed 'Set' call. Identical to SetGet2::set.
+ */
+ static bool set( const ObjId& dest, const string& field,
+ L index, A arg )
+ {
+ string temp = "set" + field;
+ temp[3] = std::toupper( temp[3] );
+ return SetGet2< L, A >::set( dest, temp, index, arg );
+ }
+
+ /**
+ * This setVec assigns goes through each object entry in the
+ * destId, and assigns the corresponding index and argument to it.
+ */
+ static bool setVec( Id destId, const string& field,
+ const vector< L >& index, const vector< A >& arg )
+ {
+ string temp = "set" + field;
+ temp[3] = std::toupper( temp[3] );
+ return SetGet2< L, A >::setVec( destId, temp, index, arg );
+ }
+
+ /**
+ * This setVec takes a specific object entry, presumably one with
+ * an array of values within it. The it goes through each specified
+ * index and assigns the corresponding argument.
+ * This is a brute-force assignment.
+ */
+ static bool setVec( ObjId dest, const string& field,
+ const vector< L >& index, const vector< A >& arg )
+ {
+ string temp = "set" + field;
+ temp[3] = std::toupper( temp[3] );
+ return SetGet2< L, A >::setVec( dest, temp, index, arg );
+ }
+
+ /**
+ * Faking setRepeat too. Just plugs into setVec.
+ */
+ static bool setRepeat( Id destId, const string& field,
+ const vector< L >& index, A arg )
+ {
+ vector< A > avec( index.size(), arg );
+ return setVec( destId, field, index, avec );
+ }
+
+ /**
+ * Blocking call using string conversion
+ */
+ static bool innerStrSet( const ObjId& dest, const string& field,
+ const string& indexStr, const string& val )
+ {
+ L index;
+ Conv< L >::str2val( index, indexStr );
+
+ A arg;
+ // Do NOT add 'set_' to the field name, as the 'set' func
+ // does it anyway.
+ Conv< A >::str2val( arg, val );
+ return set( dest, field, index, arg );
+ }
+
+ /**
+ * Gets a value on a specific object, looking it up using the
+ * provided index.
+ */
+ // Returns a field value.
+ static A get( const ObjId& dest, const string& field, L index )
+ {
+ ObjId tgt( dest );
+ FuncId fid;
+ string fullFieldName = "get" + field;
+ fullFieldName[3] = std::toupper( fullFieldName[3] );
+ const OpFunc* func = SetGet::checkSet( fullFieldName, tgt, fid);
+ const LookupGetOpFuncBase< L, A >* gof =
+ dynamic_cast< const LookupGetOpFuncBase< L, A >* >( func );
+ if ( gof )
+ {
+ if ( tgt.isDataHere() )
+ {
+ return gof->returnOp( tgt.eref(), index );
+ }
+ else
+ {
+ /*
+ const OpFunc* op2 = gof->makeHopFunc(
+ HopIndex( gof->opIndex(), MooseGetHop ), index );
+ const OpFunc1Base< A* >* hop =
+ dynamic_cast< const OpFunc1Base< A* >* >( op2 );
+ */
+ cout << "Warning: LookupField::get: cannot cross nodes yet\n";
+ return A();
+ /*
+ assert( hop );
+ // Blocking function.
+ hop->op( tgt.eref(), &ret );
+ delete op2;
+ return ret;
+ */
+ }
+ }
+ cout << "LookupField::get: Warning: Field::Get conversion error for " <<
+ dest.id.path() << "." << field << endl;
+ return A();
+ }
+
+ /**
+ * Blocking call that returns a vector of values in vec.
+ * This variant goes through each target object entry on dest,
+ * and passes in the same lookup index to each one. The results
+ * are put together in the vector vec.
+ */
+ static void getVec( Id dest, const string& field,
+ vector< L >& index, vector< A >& vec )
+ {
+ vec.resize( 0 );
+ ObjId tgt( dest );
+ FuncId fid;
+ string fullFieldName = "get" + field;
+ fullFieldName[3] = std::toupper( fullFieldName[3] );
+ const OpFunc* func = SetGet::checkSet( fullFieldName, tgt, fid );
+ const LookupGetOpFuncBase< L, A >* gof =
+ dynamic_cast< const LookupGetOpFuncBase< L, A >* >( func );
+ if ( gof )
+ {
+ Element* elm = dest.element();
+ unsigned int size = vec.size(); // temporary. See SetVec.
+ vec.resize( size );
+ for ( unsigned int i = 0; i < size; ++i )
+ {
+ Eref e( elm, i );
+ vec[i] = gof->returnOp( e, index );
+ }
+ return;
+ }
+ cout << "Warning: Field::getVec conversion error for " <<
+ dest.path() << endl;
+ }
+
+ /**
+ * Blocking virtual call for finding a value and returning in a
+ * string.
+ */
+ static bool innerStrGet( const ObjId& dest, const string& field,
+ const string& indexStr, string& str )
+ {
+ L index;
+ Conv< L >::str2val( index, indexStr );
+
+ A ret = get( dest, field, index );
+ Conv<A>::val2str( str, ret );
+ return 1;
+ }
};
/**
@@ -616,60 +656,66 @@ template< class L, class A > class LookupField: public SetGet2< L, A >
*/
template< class A1, class A2, class A3 > class SetGet3: public SetGet
{
- public:
- SetGet3()
- {;}
-
- /**
- * Blocking, typed 'Set' call
- */
- static bool set( const ObjId& dest, const string& field,
- A1 arg1, A2 arg2, A3 arg3 )
- {
- FuncId fid;
- ObjId tgt( dest );
- const OpFunc* func = checkSet( field, tgt, fid );
- const OpFunc3Base< A1, A2, A3 >* op =
- dynamic_cast< const OpFunc3Base< A1, A2, A3 >* >( func);
- if ( op ) {
- if ( tgt.isOffNode() ) {
- const OpFunc* op2 = op->makeHopFunc(
- HopIndex( op->opIndex(), MooseSetHop ) );
- const OpFunc3Base< A1, A2, A3 >* hop =
- dynamic_cast< const OpFunc3Base< A1, A2, A3 >* >(
- op2 );
- hop->op( tgt.eref(), arg1, arg2, arg3 );
- delete op2;
- if ( tgt.isGlobal() )
- op->op( tgt.eref(), arg1, arg2, arg3 );
- return true;
- } else {
- op->op( tgt.eref(), arg1, arg2, arg3 );
- return true;
- }
- }
- return 0;
- }
-
- /**
- * Blocking call using string conversion.
- * As yet we don't have 2 arg conversion from a single string.
- * So this is a dummy
- */
- static bool innerStrSet( const ObjId& dest, const string& field,
- const string& val )
- {
- A1 arg1;
- A2 arg2;
- A3 arg3;
- string::size_type pos = val.find_first_of( "," );
- Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
- string temp = val.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A2 >::str2val( arg2, temp.substr( 0,pos ) );
- Conv< A3 >::str2val( arg3, temp.substr( pos + 1 ) );
- return set( dest, field, arg1, arg2, arg3 );
- }
+public:
+ SetGet3()
+ {
+ ;
+ }
+
+ /**
+ * Blocking, typed 'Set' call
+ */
+ static bool set( const ObjId& dest, const string& field,
+ A1 arg1, A2 arg2, A3 arg3 )
+ {
+ FuncId fid;
+ ObjId tgt( dest );
+ const OpFunc* func = checkSet( field, tgt, fid );
+ const OpFunc3Base< A1, A2, A3 >* op =
+ dynamic_cast< const OpFunc3Base< A1, A2, A3 >* >( func);
+ if ( op )
+ {
+ if ( tgt.isOffNode() )
+ {
+ const OpFunc* op2 = op->makeHopFunc(
+ HopIndex( op->opIndex(), MooseSetHop ) );
+ const OpFunc3Base< A1, A2, A3 >* hop =
+ dynamic_cast< const OpFunc3Base< A1, A2, A3 >* >(
+ op2 );
+ hop->op( tgt.eref(), arg1, arg2, arg3 );
+ delete op2;
+ if ( tgt.isGlobal() )
+ op->op( tgt.eref(), arg1, arg2, arg3 );
+ return true;
+ }
+ else
+ {
+ op->op( tgt.eref(), arg1, arg2, arg3 );
+ return true;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Blocking call using string conversion.
+ * As yet we don't have 2 arg conversion from a single string.
+ * So this is a dummy
+ */
+ static bool innerStrSet( const ObjId& dest, const string& field,
+ const string& val )
+ {
+ A1 arg1;
+ A2 arg2;
+ A3 arg3;
+ string::size_type pos = val.find_first_of( "," );
+ Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
+ string temp = val.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A2 >::str2val( arg2, temp.substr( 0,pos ) );
+ Conv< A3 >::str2val( arg3, temp.substr( pos + 1 ) );
+ return set( dest, field, arg1, arg2, arg3 );
+ }
};
/**
@@ -677,200 +723,218 @@ template< class A1, class A2, class A3 > class SetGet3: public SetGet
*/
template< class A1, class A2, class A3, class A4 > class SetGet4: public SetGet
{
- public:
- SetGet4()
- {;}
-
- /**
- * Blocking, typed 'Set' call
- */
- static bool set( const ObjId& dest, const string& field,
- A1 arg1, A2 arg2, A3 arg3, A4 arg4 )
- {
- FuncId fid;
- ObjId tgt( dest );
- const OpFunc* func = checkSet( field, tgt, fid );
- const OpFunc4Base< A1, A2, A3, A4 >* op =
- dynamic_cast< const OpFunc4Base< A1, A2, A3, A4 >* >( func);
- if ( op ) {
- if ( tgt.isOffNode() ) {
- const OpFunc* op2 = op->makeHopFunc(
- HopIndex( op->opIndex(), MooseSetHop ) );
- const OpFunc4Base< A1, A2, A3, A4 >* hop =
- dynamic_cast< const OpFunc4Base< A1, A2, A3, A4 >* >( op2 );
- hop->op( tgt.eref(), arg1, arg2, arg3, arg4 );
- delete op2;
- if ( tgt.isGlobal() )
- op->op( tgt.eref(), arg1, arg2, arg3, arg4 );
- return true;
- } else {
- op->op( tgt.eref(), arg1, arg2, arg3, arg4 );
- return true;
- }
- }
- return 0;
- }
-
- /**
- * Blocking call using string conversion.
- * As yet we don't have 2 arg conversion from a single string.
- * So this is a dummy
- */
- static bool innerStrSet( const ObjId& dest, const string& field,
- const string& val )
- {
- A1 arg1;
- A2 arg2;
- A3 arg3;
- A4 arg4;
- string::size_type pos = val.find_first_of( "," );
- Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
- string temp = val.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A2 >::str2val( arg2, temp.substr( 0, pos ) );
- temp = temp.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A3 >::str2val( arg3, temp.substr( 0, pos ) );
- Conv< A4 >::str2val( arg4, temp.substr( pos + 1 ) );
- return set( dest, field, arg1, arg2, arg3, arg4 );
- }
+public:
+ SetGet4()
+ {
+ ;
+ }
+
+ /**
+ * Blocking, typed 'Set' call
+ */
+ static bool set( const ObjId& dest, const string& field,
+ A1 arg1, A2 arg2, A3 arg3, A4 arg4 )
+ {
+ FuncId fid;
+ ObjId tgt( dest );
+ const OpFunc* func = checkSet( field, tgt, fid );
+ const OpFunc4Base< A1, A2, A3, A4 >* op =
+ dynamic_cast< const OpFunc4Base< A1, A2, A3, A4 >* >( func);
+ if ( op )
+ {
+ if ( tgt.isOffNode() )
+ {
+ const OpFunc* op2 = op->makeHopFunc(
+ HopIndex( op->opIndex(), MooseSetHop ) );
+ const OpFunc4Base< A1, A2, A3, A4 >* hop =
+ dynamic_cast< const OpFunc4Base< A1, A2, A3, A4 >* >( op2 );
+ hop->op( tgt.eref(), arg1, arg2, arg3, arg4 );
+ delete op2;
+ if ( tgt.isGlobal() )
+ op->op( tgt.eref(), arg1, arg2, arg3, arg4 );
+ return true;
+ }
+ else
+ {
+ op->op( tgt.eref(), arg1, arg2, arg3, arg4 );
+ return true;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Blocking call using string conversion.
+ * As yet we don't have 2 arg conversion from a single string.
+ * So this is a dummy
+ */
+ static bool innerStrSet( const ObjId& dest, const string& field,
+ const string& val )
+ {
+ A1 arg1;
+ A2 arg2;
+ A3 arg3;
+ A4 arg4;
+ string::size_type pos = val.find_first_of( "," );
+ Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
+ string temp = val.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A2 >::str2val( arg2, temp.substr( 0, pos ) );
+ temp = temp.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A3 >::str2val( arg3, temp.substr( 0, pos ) );
+ Conv< A4 >::str2val( arg4, temp.substr( pos + 1 ) );
+ return set( dest, field, arg1, arg2, arg3, arg4 );
+ }
};
/**
* SetGet5 handles 5-argument Sets. It does not deal with Gets.
*/
template< class A1, class A2, class A3, class A4, class A5 > class SetGet5:
- public SetGet
+ public SetGet
{
- public:
- SetGet5()
- {;}
-
- static bool set( const ObjId& dest, const string& field,
- A1 arg1, A2 arg2, A3 arg3, A4 arg4, A5 arg5 )
- {
- FuncId fid;
- ObjId tgt( dest );
- const OpFunc* func = checkSet( field, tgt, fid );
- const OpFunc5Base< A1, A2, A3, A4, A5 >* op =
- dynamic_cast< const OpFunc5Base< A1, A2, A3, A4, A5 >* >( func);
- if ( op ) {
- if ( tgt.isOffNode() ) {
- const OpFunc* op2 = op->makeHopFunc(
- HopIndex( op->opIndex(), MooseSetHop ) );
- const OpFunc5Base< A1, A2, A3, A4, A5 >* hop =
- dynamic_cast< const OpFunc5Base< A1, A2, A3, A4, A5 >* >( op2 );
- hop->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5 );
- delete op2;
- if ( tgt.isGlobal() )
- op->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5 );
- return true;
- } else {
- op->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5 );
- return true;
- }
- }
- return 0;
- }
-
- /**
- * Blocking call using string conversion.
- * As yet we don't have 2 arg conversion from a single string.
- * So this is a dummy
- */
- static bool innerStrSet( const ObjId& dest, const string& field,
- const string& val )
- {
- A1 arg1;
- A2 arg2;
- A3 arg3;
- A4 arg4;
- A5 arg5;
- string::size_type pos = val.find_first_of( "," );
- Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
- string temp = val.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A2 >::str2val( arg2, temp.substr( 0, pos ) );
- temp = temp.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A3 >::str2val( arg3, temp.substr( 0, pos ) );
- temp = temp.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A4 >::str2val( arg4, temp.substr( 0, pos ) );
- Conv< A5 >::str2val( arg5, temp.substr( pos + 1 ) );
- return set( dest, field, arg1, arg2, arg3, arg4, arg5 );
- }
+public:
+ SetGet5()
+ {
+ ;
+ }
+
+ static bool set( const ObjId& dest, const string& field,
+ A1 arg1, A2 arg2, A3 arg3, A4 arg4, A5 arg5 )
+ {
+ FuncId fid;
+ ObjId tgt( dest );
+ const OpFunc* func = checkSet( field, tgt, fid );
+ const OpFunc5Base< A1, A2, A3, A4, A5 >* op =
+ dynamic_cast< const OpFunc5Base< A1, A2, A3, A4, A5 >* >( func);
+ if ( op )
+ {
+ if ( tgt.isOffNode() )
+ {
+ const OpFunc* op2 = op->makeHopFunc(
+ HopIndex( op->opIndex(), MooseSetHop ) );
+ const OpFunc5Base< A1, A2, A3, A4, A5 >* hop =
+ dynamic_cast< const OpFunc5Base< A1, A2, A3, A4, A5 >* >( op2 );
+ hop->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5 );
+ delete op2;
+ if ( tgt.isGlobal() )
+ op->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5 );
+ return true;
+ }
+ else
+ {
+ op->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5 );
+ return true;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Blocking call using string conversion.
+ * As yet we don't have 2 arg conversion from a single string.
+ * So this is a dummy
+ */
+ static bool innerStrSet( const ObjId& dest, const string& field,
+ const string& val )
+ {
+ A1 arg1;
+ A2 arg2;
+ A3 arg3;
+ A4 arg4;
+ A5 arg5;
+ string::size_type pos = val.find_first_of( "," );
+ Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
+ string temp = val.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A2 >::str2val( arg2, temp.substr( 0, pos ) );
+ temp = temp.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A3 >::str2val( arg3, temp.substr( 0, pos ) );
+ temp = temp.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A4 >::str2val( arg4, temp.substr( 0, pos ) );
+ Conv< A5 >::str2val( arg5, temp.substr( pos + 1 ) );
+ return set( dest, field, arg1, arg2, arg3, arg4, arg5 );
+ }
};
/**
* SetGet6 handles 6-argument Sets. It does not deal with Gets.
*/
template< class A1, class A2, class A3, class A4, class A5, class A6 > class SetGet6:
- public SetGet
+ public SetGet
{
- public:
- SetGet6()
- {;}
-
- /**
- * Blocking, typed 'Set' call
- */
- static bool set( const ObjId& dest, const string& field,
- A1 arg1, A2 arg2, A3 arg3, A4 arg4, A5 arg5, A6 arg6 )
- {
- FuncId fid;
- ObjId tgt( dest );
- const OpFunc* func = checkSet( field, tgt, fid );
- const OpFunc6Base< A1, A2, A3, A4, A5, A6 >* op =
- dynamic_cast< const OpFunc6Base< A1, A2, A3, A4, A5, A6 >* >( func);
- if ( op ) {
- if ( tgt.isOffNode() ) {
- const OpFunc* op2 = op->makeHopFunc(
- HopIndex( op->opIndex(), MooseSetHop ) );
- const OpFunc6Base< A1, A2, A3, A4, A5, A6 >* hop =
- dynamic_cast< const OpFunc6Base< A1, A2, A3, A4, A5, A6 >* >( op2 );
- hop->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5, arg6 );
- delete op2;
- if ( tgt.isGlobal() )
- op->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5, arg6 );
- return true;
- } else {
- op->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5, arg6);
- return true;
- }
- }
- return 0;
- }
-
- /**
- * Blocking call using string conversion.
- */
- static bool innerStrSet( const ObjId& dest, const string& field,
- const string& val )
- {
- A1 arg1;
- A2 arg2;
- A3 arg3;
- A4 arg4;
- A5 arg5;
- A6 arg6;
- string::size_type pos = val.find_first_of( "," );
- Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
- string temp = val.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A2 >::str2val( arg2, temp.substr( 0, pos ) );
- temp = temp.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A3 >::str2val( arg3, temp.substr( 0, pos ) );
- temp = temp.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A4 >::str2val( arg4, temp.substr( 0, pos ) );
- temp = temp.substr( pos + 1 );
- pos = temp.find_first_of( "," );
- Conv< A5 >::str2val( arg5, temp.substr( 0, pos ) );
- Conv< A6 >::str2val( arg6, temp.substr( pos + 1 ) );
- return set( dest, field, arg1, arg2, arg3, arg4, arg5, arg6 );
- }
+public:
+ SetGet6()
+ {
+ ;
+ }
+
+ /**
+ * Blocking, typed 'Set' call
+ */
+ static bool set( const ObjId& dest, const string& field,
+ A1 arg1, A2 arg2, A3 arg3, A4 arg4, A5 arg5, A6 arg6 )
+ {
+ FuncId fid;
+ ObjId tgt( dest );
+ const OpFunc* func = checkSet( field, tgt, fid );
+ const OpFunc6Base< A1, A2, A3, A4, A5, A6 >* op =
+ dynamic_cast< const OpFunc6Base< A1, A2, A3, A4, A5, A6 >* >( func);
+ if ( op )
+ {
+ if ( tgt.isOffNode() )
+ {
+ const OpFunc* op2 = op->makeHopFunc(
+ HopIndex( op->opIndex(), MooseSetHop ) );
+ const OpFunc6Base< A1, A2, A3, A4, A5, A6 >* hop =
+ dynamic_cast< const OpFunc6Base< A1, A2, A3, A4, A5, A6 >* >( op2 );
+ hop->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5, arg6 );
+ delete op2;
+ if ( tgt.isGlobal() )
+ op->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5, arg6 );
+ return true;
+ }
+ else
+ {
+ op->op( tgt.eref(), arg1, arg2, arg3, arg4, arg5, arg6);
+ return true;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Blocking call using string conversion.
+ */
+ static bool innerStrSet( const ObjId& dest, const string& field,
+ const string& val )
+ {
+ A1 arg1;
+ A2 arg2;
+ A3 arg3;
+ A4 arg4;
+ A5 arg5;
+ A6 arg6;
+ string::size_type pos = val.find_first_of( "," );
+ Conv< A1 >::str2val( arg1, val.substr( 0, pos ) );
+ string temp = val.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A2 >::str2val( arg2, temp.substr( 0, pos ) );
+ temp = temp.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A3 >::str2val( arg3, temp.substr( 0, pos ) );
+ temp = temp.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A4 >::str2val( arg4, temp.substr( 0, pos ) );
+ temp = temp.substr( pos + 1 );
+ pos = temp.find_first_of( "," );
+ Conv< A5 >::str2val( arg5, temp.substr( 0, pos ) );
+ Conv< A6 >::str2val( arg6, temp.substr( pos + 1 ) );
+ return set( dest, field, arg1, arg2, arg3, arg4, arg5, arg6 );
+ }
};
#endif // _SETGET_H
diff --git a/moose-core/biophysics/CaConcBase.cpp b/moose-core/biophysics/CaConcBase.cpp
index c95c386a86bc6f8687d3537391b405a9abd94da3..1f974bb30579fdc701a89dd92e702905a4520b05 100644
--- a/moose-core/biophysics/CaConcBase.cpp
+++ b/moose-core/biophysics/CaConcBase.cpp
@@ -12,6 +12,8 @@
#include "../basecode/ElementValueFinfo.h"
#include "CaConcBase.h"
+#define VALENCE 2
+
///////////////////////////////////////////////////////
// MsgSrc definitions
///////////////////////////////////////////////////////
@@ -76,7 +78,7 @@ const Cinfo* CaConcBase::initCinfo()
"Volume scaling factor. "
"Deprecated. This is a legacy field from GENESIS and exposes "
"internal calculations. Please do not use. \n"
- "B = 1/(vol * F) so that it obeys:\n"
+ "B = 1/(vol * F* VALENCE) so that it obeys:\n"
"dC/dt = B*I_Ca - C/tau",
&CaConcBase::setB,
&CaConcBase::getB
@@ -260,7 +262,7 @@ void CaConcBase::updateDimensions( const Eref& e )
double coreRadius = diameter_ / 2.0 - thickness_;
vol -= PI * coreRadius * coreRadius * length_;
}
- double B = 1.0 / ( FaradayConst * vol );
+ double B = 1.0 / ( VALENCE* FaradayConst * vol );
vSetB( e, B );
}
diff --git a/moose-core/biophysics/HHGate.cpp b/moose-core/biophysics/HHGate.cpp
index 0e8ca5841a37cf2603dc1c20c4c02cc31478c06b..eadfeca86fbdfa864bc7496e58eec66523600c00 100644
--- a/moose-core/biophysics/HHGate.cpp
+++ b/moose-core/biophysics/HHGate.cpp
@@ -15,209 +15,209 @@ static const double SINGULARITY = 1.0e-6;
const Cinfo* HHGate::initCinfo()
{
- ///////////////////////////////////////////////////////
- // Field definitions.
- ///////////////////////////////////////////////////////
- static ReadOnlyLookupValueFinfo< HHGate, double, double > A( "A",
- "lookupA: Look up the A gate value from a double. Usually does"
- "so by direct scaling and offset to an integer lookup, using"
- "a fine enough table granularity that there is little error."
- "Alternatively uses linear interpolation."
- "The range of the double is predefined based on knowledge of"
- "voltage or conc ranges, and the granularity is specified by"
- "the xmin, xmax, and dV fields.",
- &HHGate::lookupA );
- static ReadOnlyLookupValueFinfo< HHGate, double, double > B( "B",
- "lookupB: Look up the B gate value from a double."
- "Note that this looks up the raw tables, which are transformed"
- "from the reference parameters.",
- &HHGate::lookupB );
-
- static ElementValueFinfo< HHGate, vector< double > > alpha( "alpha",
- "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",
- &HHGate::setAlpha,
- &HHGate::getAlpha
- );
-
- static ElementValueFinfo< HHGate, vector< double > > beta( "beta",
- "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",
- &HHGate::setBeta,
- &HHGate::getBeta
- );
-
- static ElementValueFinfo< HHGate, vector< double > > tau( "tau",
- "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))",
- &HHGate::setTau,
- &HHGate::getTau
- );
-
- static ElementValueFinfo< HHGate, vector< double > > mInfinity(
- "mInfinity",
- "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",
- &HHGate::setMinfinity,
- &HHGate::getMinfinity
- );
-
- static ElementValueFinfo< HHGate, double > min( "min",
- "Minimum range for lookup",
- &HHGate::setMin,
- &HHGate::getMin
- );
-
- static ElementValueFinfo< HHGate, double > max( "max",
- "Minimum range for lookup",
- &HHGate::setMax,
- &HHGate::getMax
- );
-
- static ElementValueFinfo< HHGate, unsigned int > divs( "divs",
- "Divisions for lookup. Zero means to use linear interpolation",
- &HHGate::setDivs,
- &HHGate::getDivs
- );
-
- static ElementValueFinfo< HHGate, vector< double > > tableA(
- "tableA",
- "Table of A entries",
- &HHGate::setTableA,
- &HHGate::getTableA
- );
-
- static ElementValueFinfo< HHGate, vector< double > > tableB(
- "tableB",
- "Table of alpha + beta entries",
- &HHGate::setTableB,
- &HHGate::getTableB
- );
-
- static ElementValueFinfo< HHGate, bool > useInterpolation(
- "useInterpolation",
- "Flag: use linear interpolation if true, else direct lookup",
- &HHGate::setUseInterpolation,
- &HHGate::getUseInterpolation
- );
-
- static ElementValueFinfo< HHGate, vector< double > > alphaParms(
- "alphaParms",
- "Set up both gates using 13 parameters, as follows:"
- "setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmax"
- "Here AA-AF are Coefficients A to F of the alpha (forward) term"
- "Here BA-BF are Coefficients A to F of the beta (reverse) term"
- "Here 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",
- &HHGate::setupAlpha,
- &HHGate::getAlphaParms
- );
-
- ///////////////////////////////////////////////////////
- // DestFinfos
- ///////////////////////////////////////////////////////
- static DestFinfo setupAlpha( "setupAlpha",
- "Set up both gates using 13 parameters, as follows:"
- "setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmax"
- "Here AA-AF are Coefficients A to F of the alpha (forward) term"
- "Here BA-BF are Coefficients A to F of the beta (reverse) term"
- "Here 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",
- new EpFunc1< HHGate, vector< double > >( &HHGate::setupAlpha )
- );
- static DestFinfo setupTau( "setupTau",
- "Identical to setupAlpha, except that the forms specified by"
- "the 13 parameters are for the tau and m-infinity curves rather"
- "than the alpha and beta terms. So the parameters are:"
- "setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmax"
- "As before, the equation describing each curve is:"
- "y(x) = (A + B * x) / (C + exp((x + D) / F))",
- new EpFunc1< HHGate, vector< double > >( &HHGate::setupTau )
- );
- static DestFinfo tweakAlpha( "tweakAlpha",
- "Dummy function for backward compatibility. It used to convert"
- "the tables from alpha, beta values to alpha, alpha+beta"
- "because the internal calculations used these forms. Not"
- "needed now, deprecated.",
- new OpFunc0< HHGate >( &HHGate::tweakAlpha )
- );
- static DestFinfo tweakTau( "tweakTau",
- "Dummy function for backward compatibility. It used to convert"
- "the tables from tau, minf values to alpha, alpha+beta"
- "because the internal calculations used these forms. Not"
- "needed now, deprecated.",
- new OpFunc0< HHGate >( &HHGate::tweakTau )
- );
- static DestFinfo setupGate( "setupGate",
- "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_beta"
- "This sets up the gate using the equation:"
- "y(x) = (A + B * x) / (C + exp((x + D) / F))"
- "Deprecated.",
- new EpFunc1< HHGate, vector< double > >( &HHGate::setupGate )
- );
- static Finfo* HHGateFinfos[] =
- {
- &A, // ReadOnlyLookupValue
- &B, // ReadOnlyLookupValue
- &alpha, // ElementValue
- &beta, // ElementValue
- &tau, // ElementValue
- &mInfinity, // ElementValue
- &min, // ElementValue
- &max, // ElementValue
- &divs, // ElementValue
- &tableA, // ElementValue
- &tableB, // ElementValue
- &useInterpolation, // ElementValue
- &alphaParms, // ElementValue
- &setupAlpha, // Dest
- &setupTau, // Dest
- &tweakAlpha, // Dest
- &tweakTau, // Dest
- &setupGate, // Dest
+ ///////////////////////////////////////////////////////
+ // Field definitions.
+ ///////////////////////////////////////////////////////
+ static ReadOnlyLookupValueFinfo< HHGate, double, double > A( "A",
+ "lookupA: Look up the A gate value from a double. Usually does"
+ "so by direct scaling and offset to an integer lookup, using"
+ "a fine enough table granularity that there is little error."
+ "Alternatively uses linear interpolation."
+ "The range of the double is predefined based on knowledge of"
+ "voltage or conc ranges, and the granularity is specified by"
+ "the xmin, xmax, and dV fields.",
+ &HHGate::lookupA );
+ static ReadOnlyLookupValueFinfo< HHGate, double, double > B( "B",
+ "lookupB: Look up the B gate value from a double."
+ "Note that this looks up the raw tables, which are transformed"
+ "from the reference parameters.",
+ &HHGate::lookupB );
+
+ static ElementValueFinfo< HHGate, vector< double > > alpha( "alpha",
+ "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",
+ &HHGate::setAlpha,
+ &HHGate::getAlpha
+ );
+
+ static ElementValueFinfo< HHGate, vector< double > > beta( "beta",
+ "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",
+ &HHGate::setBeta,
+ &HHGate::getBeta
+ );
+
+ static ElementValueFinfo< HHGate, vector< double > > tau( "tau",
+ "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))",
+ &HHGate::setTau,
+ &HHGate::getTau
+ );
+
+ static ElementValueFinfo< HHGate, vector< double > > mInfinity(
+ "mInfinity",
+ "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",
+ &HHGate::setMinfinity,
+ &HHGate::getMinfinity
+ );
+
+ static ElementValueFinfo< HHGate, double > min( "min",
+ "Minimum range for lookup",
+ &HHGate::setMin,
+ &HHGate::getMin
+ );
+
+ static ElementValueFinfo< HHGate, double > max( "max",
+ "Minimum range for lookup",
+ &HHGate::setMax,
+ &HHGate::getMax
+ );
+
+ static ElementValueFinfo< HHGate, unsigned int > divs( "divs",
+ "Divisions for lookup. Zero means to use linear interpolation",
+ &HHGate::setDivs,
+ &HHGate::getDivs
+ );
+
+ static ElementValueFinfo< HHGate, vector< double > > tableA(
+ "tableA",
+ "Table of A entries",
+ &HHGate::setTableA,
+ &HHGate::getTableA
+ );
+
+ static ElementValueFinfo< HHGate, vector< double > > tableB(
+ "tableB",
+ "Table of alpha + beta entries",
+ &HHGate::setTableB,
+ &HHGate::getTableB
+ );
+
+ static ElementValueFinfo< HHGate, bool > useInterpolation(
+ "useInterpolation",
+ "Flag: use linear interpolation if true, else direct lookup",
+ &HHGate::setUseInterpolation,
+ &HHGate::getUseInterpolation
+ );
+
+ static ElementValueFinfo< HHGate, vector< double > > alphaParms(
+ "alphaParms",
+ "Set up both gates using 13 parameters, as follows:"
+ "setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmax"
+ "Here AA-AF are Coefficients A to F of the alpha (forward) term"
+ "Here BA-BF are Coefficients A to F of the beta (reverse) term"
+ "Here 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",
+ &HHGate::setupAlpha,
+ &HHGate::getAlphaParms
+ );
+
+ ///////////////////////////////////////////////////////
+ // DestFinfos
+ ///////////////////////////////////////////////////////
+ static DestFinfo setupAlpha( "setupAlpha",
+ "Set up both gates using 13 parameters, as follows:"
+ "setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmax"
+ "Here AA-AF are Coefficients A to F of the alpha (forward) term"
+ "Here BA-BF are Coefficients A to F of the beta (reverse) term"
+ "Here 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",
+ new EpFunc1< HHGate, vector< double > >( &HHGate::setupAlpha )
+ );
+ static DestFinfo setupTau( "setupTau",
+ "Identical to setupAlpha, except that the forms specified by"
+ "the 13 parameters are for the tau and m-infinity curves rather"
+ "than the alpha and beta terms. So the parameters are:"
+ "setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmax"
+ "As before, the equation describing each curve is:"
+ "y(x) = (A + B * x) / (C + exp((x + D) / F))",
+ new EpFunc1< HHGate, vector< double > >( &HHGate::setupTau )
+ );
+ static DestFinfo tweakAlpha( "tweakAlpha",
+ "Dummy function for backward compatibility. It used to convert"
+ "the tables from alpha, beta values to alpha, alpha+beta"
+ "because the internal calculations used these forms. Not"
+ "needed now, deprecated.",
+ new OpFunc0< HHGate >( &HHGate::tweakAlpha )
+ );
+ static DestFinfo tweakTau( "tweakTau",
+ "Dummy function for backward compatibility. It used to convert"
+ "the tables from tau, minf values to alpha, alpha+beta"
+ "because the internal calculations used these forms. Not"
+ "needed now, deprecated.",
+ new OpFunc0< HHGate >( &HHGate::tweakTau )
+ );
+ static DestFinfo setupGate( "setupGate",
+ "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_beta"
+ "This sets up the gate using the equation:"
+ "y(x) = (A + B * x) / (C + exp((x + D) / F))"
+ "Deprecated.",
+ new EpFunc1< HHGate, vector< double > >( &HHGate::setupGate )
+ );
+ static Finfo* HHGateFinfos[] =
+ {
+ &A, // ReadOnlyLookupValue
+ &B, // ReadOnlyLookupValue
+ &alpha, // ElementValue
+ &beta, // ElementValue
+ &tau, // ElementValue
+ &mInfinity, // ElementValue
+ &min, // ElementValue
+ &max, // ElementValue
+ &divs, // ElementValue
+ &tableA, // ElementValue
+ &tableB, // ElementValue
+ &useInterpolation, // ElementValue
+ &alphaParms, // ElementValue
+ &setupAlpha, // Dest
+ &setupTau, // Dest
+ &tweakAlpha, // Dest
+ &tweakTau, // Dest
+ &setupGate, // Dest
};
- static string doc[] =
+ static string doc[] =
{
- "Name", "HHGate",
- "Author", "Upinder S. Bhalla, 2011, NCBS",
- "Description", "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.",
+ "Name", "HHGate",
+ "Author", "Upinder S. Bhalla, 2011, NCBS",
+ "Description", "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.",
};
- static Dinfo< HHGate > dinfo;
- static Cinfo HHGateCinfo(
- "HHGate",
- Neutral::initCinfo(),
- HHGateFinfos, sizeof(HHGateFinfos)/sizeof(Finfo *),
- &dinfo,
- doc,
- sizeof(doc)/sizeof(string)
- );
+ static Dinfo< HHGate > dinfo;
+ static Cinfo HHGateCinfo(
+ "HHGate",
+ Neutral::initCinfo(),
+ HHGateFinfos, sizeof(HHGateFinfos)/sizeof(Finfo *),
+ &dinfo,
+ doc,
+ sizeof(doc)/sizeof(string)
+ );
- return &HHGateCinfo;
+ return &HHGateCinfo;
}
static const Cinfo* hhGateCinfo = HHGate::initCinfo();
@@ -225,22 +225,22 @@ static const Cinfo* hhGateCinfo = HHGate::initCinfo();
// Core class functions
///////////////////////////////////////////////////
HHGate::HHGate()
- : xmin_(0), xmax_(1), invDx_(1),
- originalChanId_(0),
- originalGateId_(0),
- lookupByInterpolation_(0),
- isDirectTable_(0)
+ : xmin_(0), xmax_(1), invDx_(1),
+ originalChanId_(0),
+ originalGateId_(0),
+ lookupByInterpolation_(0),
+ isDirectTable_(0)
{;}
HHGate::HHGate( Id originalChanId, Id originalGateId )
- :
- A_( 1, 0.0 ),
- B_( 1, 0.0 ),
- xmin_(0), xmax_(1), invDx_(1),
- originalChanId_( originalChanId ),
- originalGateId_( originalGateId ),
- lookupByInterpolation_(0),
- isDirectTable_(0)
+ :
+ A_( 1, 0.0 ),
+ B_( 1, 0.0 ),
+ xmin_(0), xmax_(1), invDx_(1),
+ originalChanId_( originalChanId ),
+ originalGateId_( originalGateId ),
+ lookupByInterpolation_(0),
+ isDirectTable_(0)
{;}
///////////////////////////////////////////////////
@@ -249,272 +249,309 @@ HHGate::HHGate( Id originalChanId, Id originalGateId )
double HHGate::lookupTable( const vector< double >& tab, double v ) const
{
- if ( v <= xmin_ ) return tab[0];
- if ( v >= xmax_ ) return tab.back();
- if ( lookupByInterpolation_ ) {
- unsigned int index =
- static_cast< unsigned int >( ( v - xmin_ ) * invDx_ );
- assert( tab.size() > index );
- double frac = ( v - xmin_ - index / invDx_ ) * invDx_;
- return tab[ index ] * ( 1 - frac ) + tab[ index + 1 ] * frac;
- } else {
- return tab[ static_cast< unsigned int >( (v - xmin_) * invDx_ ) ];
- }
+ if ( v <= xmin_ ) return tab[0];
+ if ( v >= xmax_ ) return tab.back();
+ if ( lookupByInterpolation_ )
+ {
+ unsigned int index =
+ static_cast< unsigned int >( ( v - xmin_ ) * invDx_ );
+ assert( tab.size() > index );
+ double frac = ( v - xmin_ - index / invDx_ ) * invDx_;
+ return tab[ index ] * ( 1 - frac ) + tab[ index + 1 ] * frac;
+ }
+ else
+ {
+ return tab[ static_cast< unsigned int >( (v - xmin_) * invDx_ ) ];
+ }
}
double HHGate::lookupA( double v ) const
{
- return lookupTable( A_, v );
+ return lookupTable( A_, v );
}
double HHGate::lookupB( double v ) const
{
- return lookupTable( B_, v );
+ return lookupTable( B_, v );
}
void HHGate::lookupBoth( double v, double* A, double* B ) const
{
- if ( v <= xmin_ ) {
- *A = A_[0];
- *B = B_[0];
- } else if ( v >= xmax_ ) {
- *A = A_.back();
- *B = B_.back();
- } else {
- unsigned int index =
- static_cast< unsigned int >( ( v - xmin_ ) * invDx_ );
- assert( A_.size() > index && B_.size() > index );
- if ( lookupByInterpolation_ ) {
- double frac = ( v - xmin_ - index / invDx_ ) * invDx_;
- *A = A_[ index ] * ( 1 - frac ) + A_[ index + 1 ] * frac;
- *B = B_[ index ] * ( 1 - frac ) + B_[ index + 1 ] * frac;
- } else {
- *A = A_[ index ];
- *B = B_[ index ];
- }
- }
+ if ( v <= xmin_ )
+ {
+ *A = A_[0];
+ *B = B_[0];
+ }
+ else if ( v >= xmax_ )
+ {
+ *A = A_.back();
+ *B = B_.back();
+ }
+ else
+ {
+ unsigned int index =
+ static_cast< unsigned int >( ( v - xmin_ ) * invDx_ );
+ assert( A_.size() > index && B_.size() > index );
+ if ( lookupByInterpolation_ )
+ {
+ double frac = ( v - xmin_ - index / invDx_ ) * invDx_;
+ *A = A_[ index ] * ( 1 - frac ) + A_[ index + 1 ] * frac;
+ *B = B_[ index ] * ( 1 - frac ) + B_[ index + 1 ] * frac;
+ }
+ else
+ {
+ *A = A_[ index ];
+ *B = B_[ index ];
+ }
+ }
}
vector< double > HHGate::getAlpha( const Eref& e) const
{
- return alpha_;
+ return alpha_;
}
void HHGate::setAlpha( const Eref& e, vector< double > val )
{
- if ( val.size() != 5 ) {
- cout << "Error: HHGate::setAlpha on " << e.id().path() <<
- ": Number of entries on argument vector should be 5, was " <<
- val.size() << endl;
- return;
- }
- if ( checkOriginal( e.id(), "alpha" ) ) {
- alpha_ = val;
- updateTauMinf();
- updateTables();
- }
+ if ( val.size() != 5 )
+ {
+ cout << "Error: HHGate::setAlpha on " << e.id().path() <<
+ ": Number of entries on argument vector should be 5, was " <<
+ val.size() << endl;
+ return;
+ }
+ if ( checkOriginal( e.id(), "alpha" ) )
+ {
+ alpha_ = val;
+ updateTauMinf();
+ updateTables();
+ }
}
vector< double > HHGate::getBeta( const Eref& e) const
{
- return beta_;
+ return beta_;
}
void HHGate::setBeta( const Eref& e, vector< double > val )
{
- if ( val.size() != 5 ) {
- cout << "Error: HHGate::setBeta on " << e.id().path() <<
- ": Number of entries on argument vector should be 5, was " <<
- val.size() << endl;
- return;
- }
- if ( checkOriginal( e.id(), "beta" ) ) {
- beta_ = val;
- updateTauMinf();
- updateTables();
- }
+ if ( val.size() != 5 )
+ {
+ cout << "Error: HHGate::setBeta on " << e.id().path() <<
+ ": Number of entries on argument vector should be 5, was " <<
+ val.size() << endl;
+ return;
+ }
+ if ( checkOriginal( e.id(), "beta" ) )
+ {
+ beta_ = val;
+ updateTauMinf();
+ updateTables();
+ }
}
vector< double > HHGate::getTau( const Eref& e) const
{
- return tau_;
+ return tau_;
}
void HHGate::setTau( const Eref& e, vector< double > val )
{
- if ( val.size() != 5 ) {
- cout << "Error: HHGate::setTau on " << e.id().path() <<
- ": Number of entries on argument vector should be 5, was " <<
- val.size() << endl;
- return;
- }
- if ( checkOriginal( e.id(), "tau" ) ) {
- tau_ = val;
- updateAlphaBeta();
- updateTables();
- }
+ if ( val.size() != 5 )
+ {
+ cout << "Error: HHGate::setTau on " << e.id().path() <<
+ ": Number of entries on argument vector should be 5, was " <<
+ val.size() << endl;
+ return;
+ }
+ if ( checkOriginal( e.id(), "tau" ) )
+ {
+ tau_ = val;
+ updateAlphaBeta();
+ updateTables();
+ }
}
vector< double > HHGate::getMinfinity( const Eref& e) const
{
- return mInfinity_;
+ return mInfinity_;
}
void HHGate::setMinfinity( const Eref& e, vector< double > val )
{
- if ( val.size() != 5 ) {
- cout << "Error: HHGate::setMinfinity on " << e.id().path() <<
- ": Number of entries on argument vector should be 5, was " <<
- val.size() << endl;
- return;
- }
- if ( checkOriginal( e.id(), "mInfinity" ) ) {
- mInfinity_ = val;
- updateAlphaBeta();
- updateTables();
- }
+ if ( val.size() != 5 )
+ {
+ cout << "Error: HHGate::setMinfinity on " << e.id().path() <<
+ ": Number of entries on argument vector should be 5, was " <<
+ val.size() << endl;
+ return;
+ }
+ if ( checkOriginal( e.id(), "mInfinity" ) )
+ {
+ mInfinity_ = val;
+ updateAlphaBeta();
+ updateTables();
+ }
}
double HHGate::getMin( const Eref& e) const
{
- return xmin_;
+ return xmin_;
}
void HHGate::setMin( const Eref& e, double val )
{
- if ( checkOriginal( e.id(), "min" ) ) {
- xmin_ = val;
- unsigned int xdivs = A_.size() - 1;
- if ( isDirectTable_ && xdivs > 0 ) {
- // Stuff here to stretch out table using interpolation.
- invDx_ = static_cast< double >( xdivs ) / ( xmax_ - val );
- tabFill( A_, xdivs, val, xmax_ );
- tabFill( B_, xdivs, val, xmax_ );
- } else {
- updateTables();
+ if ( checkOriginal( e.id(), "min" ) )
+ {
+ xmin_ = val;
+ unsigned int xdivs = A_.size() - 1;
+ if ( isDirectTable_ && xdivs > 0 )
+ {
+ // Stuff here to stretch out table using interpolation.
+ invDx_ = static_cast< double >( xdivs ) / ( xmax_ - val );
+ tabFill( A_, xdivs, val, xmax_ );
+ tabFill( B_, xdivs, val, xmax_ );
+ }
+ else
+ {
+ updateTables();
+ }
}
- }
}
double HHGate::getMax( const Eref& e) const
{
- return xmax_;
+ return xmax_;
}
void HHGate::setMax( const Eref& e, double val )
{
- if ( checkOriginal( e.id(), "max" ) ) {
- xmax_ = val;
- unsigned int xdivs = A_.size() - 1;
- if ( isDirectTable_ && xdivs > 0 ) {
- // Set up using direct assignment of table values.
- invDx_ = static_cast< double >( xdivs ) / ( val - xmin_ );
- tabFill( A_, xdivs, xmin_, val );
- tabFill( B_, xdivs, xmin_, val );
- } else {
- // Set up using functional form. here we just recalculate.
- updateTables();
+ if ( checkOriginal( e.id(), "max" ) )
+ {
+ xmax_ = val;
+ unsigned int xdivs = A_.size() - 1;
+ if ( isDirectTable_ && xdivs > 0 )
+ {
+ // Set up using direct assignment of table values.
+ invDx_ = static_cast< double >( xdivs ) / ( val - xmin_ );
+ tabFill( A_, xdivs, xmin_, val );
+ tabFill( B_, xdivs, xmin_, val );
+ }
+ else
+ {
+ // Set up using functional form. here we just recalculate.
+ updateTables();
+ }
}
- }
}
unsigned int HHGate::getDivs( const Eref& e) const
{
- return A_.size() - 1;
+ return A_.size() - 1;
}
void HHGate::setDivs( const Eref& e, unsigned int val )
{
- if ( checkOriginal( e.id(), "divs" ) ) {
- if ( isDirectTable_ ) {
- invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
- tabFill( A_, val, xmin_, xmax_ );
- tabFill( B_, val, xmin_, xmax_ );
- } else {
- /// Stuff here to redo sizes.
- A_.resize( val + 1 );
- B_.resize( val + 1 );
- invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
- updateTables();
+ if ( checkOriginal( e.id(), "divs" ) )
+ {
+ if ( isDirectTable_ )
+ {
+ invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
+ tabFill( A_, val, xmin_, xmax_ );
+ tabFill( B_, val, xmin_, xmax_ );
+ }
+ else
+ {
+ /// Stuff here to redo sizes.
+ A_.resize( val + 1 );
+ B_.resize( val + 1 );
+ invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
+ updateTables();
+ }
}
- }
}
vector< double > HHGate::getTableA( const Eref& e) const
{
- return A_;
+ return A_;
}
void HHGate::setTableA( const Eref& e, vector< double > v )
{
- if ( v.size() < 2 ) {
- cout << "Warning: HHGate::setTableA: size must be >= 2 entries on "
- << e.id().path() << endl;
- return;
- }
- if ( checkOriginal( e.id(), "tableA" ) ) {
- isDirectTable_ = 1;
- A_ = v;
- unsigned int xdivs = A_.size() - 1;
- invDx_ = static_cast< double >( xdivs ) / ( xmax_ - xmin_ );
- }
+ if ( v.size() < 2 )
+ {
+ cout << "Warning: HHGate::setTableA: size must be >= 2 entries on "
+ << e.id().path() << endl;
+ return;
+ }
+ if ( checkOriginal( e.id(), "tableA" ) )
+ {
+ isDirectTable_ = 1;
+ A_ = v;
+ unsigned int xdivs = A_.size() - 1;
+ invDx_ = static_cast< double >( xdivs ) / ( xmax_ - xmin_ );
+ }
}
vector< double > HHGate::getTableB( const Eref& e) const
{
- return B_;
+ return B_;
}
void HHGate::setTableB( const Eref& e, vector< double > v )
{
- if ( checkOriginal( e.id(), "tableB" ) ) {
- isDirectTable_ = 1;
- if ( A_.size() != v.size() ) {
- cout << "Warning: HHGate::setTableB: size should be same as table A: " << v.size() << " != " << A_.size() << ". Ignoring.\n";
- return;
+ if ( checkOriginal( e.id(), "tableB" ) )
+ {
+ isDirectTable_ = 1;
+ if ( A_.size() != v.size() )
+ {
+ cout << "Warning: HHGate::setTableB: size should be same as table A: " << v.size() << " != " << A_.size() << ". Ignoring.\n";
+ return;
+ }
+ B_ = v;
}
- B_ = v;
- }
}
bool HHGate::getUseInterpolation( const Eref& e) const
{
- return lookupByInterpolation_;
+ return lookupByInterpolation_;
}
void HHGate::setUseInterpolation( const Eref& e, bool val )
{
- if ( checkOriginal( e.id(), "useInterpolation" ) )
- lookupByInterpolation_ = val;
+ if ( checkOriginal( e.id(), "useInterpolation" ) )
+ lookupByInterpolation_ = val;
}
void HHGate::setupAlpha( const Eref& e,
- vector< double > parms )
+ vector< double > parms )
{
- if ( checkOriginal( e.id(), "setupAlpha" ) ) {
- if ( parms.size() != 13 ) {
- cout << "HHGate::setupAlpha: Error: parms.size() != 13\n";
- return;
+ if ( checkOriginal( e.id(), "setupAlpha" ) )
+ {
+ if ( parms.size() != 13 )
+ {
+ cout << "HHGate::setupAlpha: Error: parms.size() != 13\n";
+ return;
+ }
+ setupTables( parms, false );
+ alpha_.resize( 5, 0 );
+ beta_.resize( 5, 0 );
+ for ( unsigned int i = 0; i < 5; ++i )
+ alpha_[i] = parms[i];
+ for ( unsigned int i = 5; i < 10; ++i )
+ beta_[i - 5] = parms[i];
}
- setupTables( parms, false );
- alpha_.resize( 5, 0 );
- beta_.resize( 5, 0 );
- for ( unsigned int i = 0; i < 5; ++i )
- alpha_[i] = parms[i];
- for ( unsigned int i = 5; i < 10; ++i )
- beta_[i - 5] = parms[i];
- }
}
vector< double > HHGate::getAlphaParms( const Eref& e ) const
{
- vector< double > ret = alpha_;
- ret.insert( ret.end(), beta_.begin(), beta_.end() );
- ret.push_back( A_.size() );
- ret.push_back( xmin_ );
- ret.push_back( xmax_ );
+ vector< double > ret = alpha_;
+ ret.insert( ret.end(), beta_.begin(), beta_.end() );
+ ret.push_back( A_.size() );
+ ret.push_back( xmin_ );
+ ret.push_back( xmax_ );
- return ret;
+ return ret;
}
///////////////////////////////////////////////////
@@ -522,25 +559,27 @@ vector< double > HHGate::getAlphaParms( const Eref& e ) const
///////////////////////////////////////////////////
void HHGate::setupTau( const Eref& e,
- vector< double > parms )
+ vector< double > parms )
{
- if ( checkOriginal( e.id(), "setupTau" ) ) {
- if ( parms.size() != 13 ) {
- cout << "HHGate::setupTau: Error: parms.size() != 13\n";
- return;
+ if ( checkOriginal( e.id(), "setupTau" ) )
+ {
+ if ( parms.size() != 13 )
+ {
+ cout << "HHGate::setupTau: Error: parms.size() != 13\n";
+ return;
+ }
+ setupTables( parms, true );
}
- setupTables( parms, true );
- }
}
void HHGate::tweakAlpha()
{
- ; // Dummy
+ ; // Dummy
}
void HHGate::tweakTau()
{
- ; // Dummy
+ ; // Dummy
}
/**
@@ -550,96 +589,114 @@ void HHGate::tweakTau()
*/
void HHGate::setupTables( const vector< double >& parms, bool doTau )
{
- assert( parms.size() == 13 );
- static const int XDIVS = 10;
- static const int XMIN = 11;
- static const int XMAX = 12;
- if ( parms[XDIVS] < 1 ) return;
- unsigned int xdivs = static_cast< unsigned int >( parms[XDIVS] );
-
- A_.resize( xdivs + 1 );
- B_.resize( xdivs + 1 );
- xmin_ = parms[XMIN];
- xmax_ = parms[XMAX];
- assert( xmax_ > xmin_ );
- invDx_ = xdivs / (xmax_ - xmin_ );
- double dx = ( xmax_ - xmin_ ) / xdivs;
-
- double x = xmin_;
- double prevAentry = 0.0;
- double prevBentry = 0.0;
- double temp;
- double temp2 = 0.0;
- unsigned int i;
-
- for( i = 0; i <= xdivs; i++ ) {
- if ( fabs( parms[4] ) < SINGULARITY ) {
- temp = 0.0;
- A_[i] = temp;
- } else {
- temp2 = parms[2] + exp( ( x + parms[3] ) / parms[4] );
- if ( fabs( temp2 ) < SINGULARITY ) {
- temp2 = parms[2] + exp( ( x + dx/10.0 + parms[3] ) / parms[4] );
- temp = ( parms[0] + parms[1] * (x + dx/10 ) ) / temp2;
-
- temp2 = parms[2] + exp( ( x - dx/10.0 + parms[3] ) / parms[4] );
- temp += ( parms[0] + parms[1] * (x - dx/10 ) ) / temp2;
- temp /= 2.0;
- // cout << "interpolated temp = " << temp << ", prev = " << prevAentry << endl;
-
- // temp = prevAentry;
- A_[i] = temp;
- } else {
- temp = ( parms[0] + parms[1] * x) / temp2;
- A_[i] = temp;
- }
- }
- if ( fabs( parms[9] ) < SINGULARITY ) {
- B_[i] = 0.0;
- } else {
- temp2 = parms[7] + exp( ( x + parms[8] ) / parms[9] );
- if ( fabs( temp2 ) < SINGULARITY ) {
- temp2 = parms[7] + exp( ( x + dx/10.0 + parms[8] ) / parms[9] );
- temp = (parms[5] + parms[6] * (x + dx/10) ) / temp2;
- temp2 = parms[7] + exp( ( x - dx/10.0 + parms[8] ) / parms[9] );
- temp += (parms[5] + parms[6] * (x - dx/10) ) / temp2;
- temp /= 2.0;
- B_[i] = temp;
- // B_[i] = prevBentry;
- } else {
- B_[i] = (parms[5] + parms[6] * x ) / temp2;
- // B_.table_[i] = ( parms[5] + parms[6] * x ) / temp2;
- }
- }
- // There are cleaner ways to do this, but this keeps
- // the relation to the GENESIS version clearer.
- // Note the additional SINGULARITY check, to fix a bug
- // in the earlier code.
- if ( doTau == 0 && fabs( temp2 ) > SINGULARITY )
- B_[i] += temp;
-
- prevAentry = A_[i];
- prevBentry = B_[i];
- x += dx;
- }
-
- prevAentry = 0.0;
- prevBentry = 0.0;
- if ( doTau ) {
- for( i = 0; i <= xdivs; i++ ) {
- temp = A_[i];
- temp2 = B_[i];
- if ( fabs( temp ) < SINGULARITY ) {
- A_[i] = prevAentry;
- B_[i] = prevBentry;
- } else {
- A_[i] = temp2 / temp;
- B_[i] = 1.0 / temp;
- }
- prevAentry = A_[i];
- prevBentry = B_[i];
- }
- }
+ assert( parms.size() == 13 );
+ static const int XDIVS = 10;
+ static const int XMIN = 11;
+ static const int XMAX = 12;
+ if ( parms[XDIVS] < 1 ) return;
+ unsigned int xdivs = static_cast< unsigned int >( parms[XDIVS] );
+
+ A_.resize( xdivs + 1 );
+ B_.resize( xdivs + 1 );
+ xmin_ = parms[XMIN];
+ xmax_ = parms[XMAX];
+ assert( xmax_ > xmin_ );
+ invDx_ = xdivs / (xmax_ - xmin_ );
+ double dx = ( xmax_ - xmin_ ) / xdivs;
+
+ double x = xmin_;
+ double prevAentry = 0.0;
+ double prevBentry = 0.0;
+ double temp;
+ double temp2 = 0.0;
+ unsigned int i;
+
+ for( i = 0; i <= xdivs; i++ )
+ {
+ if ( fabs( parms[4] ) < SINGULARITY )
+ {
+ temp = 0.0;
+ A_[i] = temp;
+ }
+ else
+ {
+ temp2 = parms[2] + exp( ( x + parms[3] ) / parms[4] );
+ if ( fabs( temp2 ) < SINGULARITY )
+ {
+ temp2 = parms[2] + exp( ( x + dx/10.0 + parms[3] ) / parms[4] );
+ temp = ( parms[0] + parms[1] * (x + dx/10 ) ) / temp2;
+
+ temp2 = parms[2] + exp( ( x - dx/10.0 + parms[3] ) / parms[4] );
+ temp += ( parms[0] + parms[1] * (x - dx/10 ) ) / temp2;
+ temp /= 2.0;
+ // cout << "interpolated temp = " << temp << ", prev = " << prevAentry << endl;
+
+ // temp = prevAentry;
+ A_[i] = temp;
+ }
+ else
+ {
+ temp = ( parms[0] + parms[1] * x) / temp2;
+ A_[i] = temp;
+ }
+ }
+ if ( fabs( parms[9] ) < SINGULARITY )
+ {
+ B_[i] = 0.0;
+ }
+ else
+ {
+ temp2 = parms[7] + exp( ( x + parms[8] ) / parms[9] );
+ if ( fabs( temp2 ) < SINGULARITY )
+ {
+ temp2 = parms[7] + exp( ( x + dx/10.0 + parms[8] ) / parms[9] );
+ temp = (parms[5] + parms[6] * (x + dx/10) ) / temp2;
+ temp2 = parms[7] + exp( ( x - dx/10.0 + parms[8] ) / parms[9] );
+ temp += (parms[5] + parms[6] * (x - dx/10) ) / temp2;
+ temp /= 2.0;
+ B_[i] = temp;
+ // B_[i] = prevBentry;
+ }
+ else
+ {
+ B_[i] = (parms[5] + parms[6] * x ) / temp2;
+ // B_.table_[i] = ( parms[5] + parms[6] * x ) / temp2;
+ }
+ }
+ // There are cleaner ways to do this, but this keeps
+ // the relation to the GENESIS version clearer.
+ // Note the additional SINGULARITY check, to fix a bug
+ // in the earlier code.
+ if ( doTau == 0 && fabs( temp2 ) > SINGULARITY )
+ B_[i] += temp;
+
+ prevAentry = A_[i];
+ prevBentry = B_[i];
+ x += dx;
+ }
+
+ prevAentry = 0.0;
+ prevBentry = 0.0;
+ if ( doTau )
+ {
+ for( i = 0; i <= xdivs; i++ )
+ {
+ temp = A_[i];
+ temp2 = B_[i];
+ if ( fabs( temp ) < SINGULARITY )
+ {
+ A_[i] = prevAentry;
+ B_[i] = prevBentry;
+ }
+ else
+ {
+ A_[i] = temp2 / temp;
+ B_[i] = 1.0 / temp;
+ }
+ prevAentry = A_[i];
+ prevBentry = B_[i];
+ }
+ }
}
/**
@@ -649,97 +706,116 @@ void HHGate::setupTables( const vector< double >& parms, bool doTau )
*/
void HHGate::tweakTables( bool doTau )
{
- unsigned int i;
- unsigned int size = A_.size();
- assert( size == B_.size() );
- if ( doTau ) {
- for ( i = 0; i < size; i++ ) {
- double temp = A_[ i ];
- double temp2 = B_[ i ];
- if ( fabs( temp ) < SINGULARITY ) {
- if ( temp < 0.0 )
- temp = -SINGULARITY;
- else
- temp = SINGULARITY;
- }
- A_[ i ] = temp2 / temp;
- B_[ i ] = 1.0 / temp;
- }
- } else {
- for ( i = 0; i < size; i++ )
- B_[i] = A_[i] + B_[i];
- }
+ unsigned int i;
+ unsigned int size = A_.size();
+ assert( size == B_.size() );
+ if ( doTau )
+ {
+ for ( i = 0; i < size; i++ )
+ {
+ double temp = A_[ i ];
+ double temp2 = B_[ i ];
+ if ( fabs( temp ) < SINGULARITY )
+ {
+ if ( temp < 0.0 )
+ temp = -SINGULARITY;
+ else
+ temp = SINGULARITY;
+ }
+ A_[ i ] = temp2 / temp;
+ B_[ i ] = 1.0 / temp;
+ }
+ }
+ else
+ {
+ for ( i = 0; i < size; i++ )
+ B_[i] = A_[i] + B_[i];
+ }
}
void HHGate::setupGate( const Eref& e,
- vector< double > parms )
-{
- // The nine arguments are :
- // A B C D F size min max isbeta
- // If size == 0 then we check that the gate has already been allocated.
- // If isbeta is true then we also have to do the conversion to
- // HHGate form of alpha, alpha+beta, assuming that the alpha gate
- // has already been setup. This uses tweakTables.
- // We may need to resize the tables if they don't match here.
- if ( !checkOriginal( e.id(), "setupGate" ) )
- return;
-
- if ( parms.size() != 9 ) {
- cout << "HHGate::setupGate: Error: parms.size() != 9\n";
- return;
- }
-
- double A = parms[0];
- double B = parms[1];
- double C = parms[2];
- double D = parms[3];
- double F = parms[4];
- int size = static_cast< int > (parms[5] );
- double min = parms[6];
- double max = parms[7];
- bool isBeta = static_cast< bool >( parms[8] );
-
- vector< double >& ip = ( isBeta ) ? B_ : A_;
-
- if ( size <= 0 ) { // Look up size, min, max from the interpol
- size = ip.size() - 1;
- if ( size <= 0 ) {
- cout << "Error: setupGate has zero size\n";
- return;
- }
- } else {
- ip.resize( size + 1 );
- }
-
- double dx = ( max - min ) / static_cast< double >( size );
- double x = min + dx / 2.0;
- for ( int i = 0; i <= size; i++ ) {
- if ( fabs ( F ) < SINGULARITY ) {
- ip[i] = 0.0;
- } else {
- double temp2 = C + exp( ( x + D ) / F );
- if ( fabs( temp2 ) < SINGULARITY )
- ip[i] = ip[i-1];
- else
- ip[i] = ( A + B * x ) / temp2;
- }
- }
-
- if ( isBeta ) {
- assert( A_.size() > 0 );
- // Here we ensure that the tables are the same size
- if ( A_.size() != B_.size() ) {
- if ( A_.size() > B_.size() ) {
- // Note that the tabFill expects to allocate the
- // terminating entry, so we put in size - 1.
- tabFill( B_, A_.size() - 1, xmin_, xmax_ );
- } else {
- tabFill( A_, B_.size() - 1, xmin_, xmax_ );
- }
- }
- // Then we do the tweaking to convert to HHChannel form.
- tweakTables( 0 );
- }
+ vector< double > parms )
+{
+ // The nine arguments are :
+ // A B C D F size min max isbeta
+ // If size == 0 then we check that the gate has already been allocated.
+ // If isbeta is true then we also have to do the conversion to
+ // HHGate form of alpha, alpha+beta, assuming that the alpha gate
+ // has already been setup. This uses tweakTables.
+ // We may need to resize the tables if they don't match here.
+ if ( !checkOriginal( e.id(), "setupGate" ) )
+ return;
+
+ if ( parms.size() != 9 )
+ {
+ cout << "HHGate::setupGate: Error: parms.size() != 9\n";
+ return;
+ }
+
+ double A = parms[0];
+ double B = parms[1];
+ double C = parms[2];
+ double D = parms[3];
+ double F = parms[4];
+ int size = static_cast< int > (parms[5] );
+ double min = parms[6];
+ double max = parms[7];
+ bool isBeta = static_cast< bool >( parms[8] );
+
+ vector< double >& ip = ( isBeta ) ? B_ : A_;
+
+ if ( size <= 0 ) // Look up size, min, max from the interpol
+ {
+ size = ip.size() - 1;
+ if ( size <= 0 )
+ {
+ cout << "Error: setupGate has zero size\n";
+ return;
+ }
+ }
+ else
+ {
+ ip.resize( size + 1 );
+ }
+
+ double dx = ( max - min ) / static_cast< double >( size );
+ double x = min + dx / 2.0;
+ for ( int i = 0; i <= size; i++ )
+ {
+ if ( fabs ( F ) < SINGULARITY )
+ {
+ ip[i] = 0.0;
+ }
+ else
+ {
+ double temp2 = C + exp( ( x + D ) / F );
+ if ( fabs( temp2 ) < SINGULARITY )
+ ip[i] = ip[i-1];
+ else
+ ip[i] = ( A + B * x ) / temp2;
+ }
+ }
+
+ if ( isBeta )
+ {
+ assert( A_.size() > 0 );
+ // Here we ensure that the tables are the same size
+ if ( A_.size() != B_.size() )
+ {
+ if ( A_.size() > B_.size() )
+ {
+ // Note that the tabFill expects to allocate the
+ // terminating entry, so we put in size - 1.
+ tabFill( B_, A_.size() - 1, xmin_, xmax_ );
+ }
+ else
+ {
+ tabFill( A_, B_.size() - 1, xmin_, xmax_ );
+ }
+ }
+ // Then we do the tweaking to convert to HHChannel form.
+ tweakTables( 0 );
+ }
}
///////////////////////////////////////////////////////////////////////
@@ -753,54 +829,56 @@ void HHGate::setupGate( const Eref& e,
* subdivisions that the table represents.
*/
void HHGate::tabFill( vector< double >& table,
- unsigned int newXdivs, double newXmin, double newXmax )
+ unsigned int newXdivs, double newXmin, double newXmax )
{
- if ( newXdivs < 3 ) {
- cout << "Error: tabFill: # divs must be >= 3. Not filling table.\n";
- return;
- }
+ if ( newXdivs < 3 )
+ {
+ cout << "Error: tabFill: # divs must be >= 3. Not filling table.\n";
+ return;
+ }
- vector< double > old = table;
- double newDx = ( newXmax - newXmin ) / newXdivs;
- table.resize( newXdivs + 1 );
- bool origLookupMode = lookupByInterpolation_;
- lookupByInterpolation_ = 1;
+ vector< double > old = table;
+ double newDx = ( newXmax - newXmin ) / newXdivs;
+ table.resize( newXdivs + 1 );
+ bool origLookupMode = lookupByInterpolation_;
+ lookupByInterpolation_ = 1;
- for( unsigned int i = 0; i <= newXdivs; ++i ) {
- table[i] = lookupTable( table, newXmin + i * newDx );
- }
+ for( unsigned int i = 0; i <= newXdivs; ++i )
+ {
+ table[i] = lookupTable( table, newXmin + i * newDx );
+ }
- lookupByInterpolation_ = origLookupMode;
+ lookupByInterpolation_ = origLookupMode;
}
bool HHGate::checkOriginal( Id id, const string& field ) const
{
- if ( id == originalGateId_ )
- return 1;
+ if ( id == originalGateId_ )
+ return 1;
- cout << "Warning: HHGate: attempt to set field '" << field << "' on " <<
- id.path() << "\nwhich is not the original Gate element. Ignored.\n";
- return 0;
+ cout << "Warning: HHGate: attempt to set field '" << field << "' on " <<
+ id.path() << "\nwhich is not the original Gate element. Ignored.\n";
+ return 0;
}
bool HHGate::isOriginalChannel( Id id ) const
{
- return ( id == originalChanId_ );
+ return ( id == originalChanId_ );
}
bool HHGate::isOriginalGate( Id id ) const
{
- return ( id == originalGateId_ );
+ return ( id == originalGateId_ );
}
Id HHGate::originalChannelId() const
{
- return originalChanId_;
+ return originalChanId_;
}
Id HHGate::originalGateId() const
{
- return originalGateId_;
+ return originalGateId_;
}
void HHGate::updateAlphaBeta()
@@ -813,13 +891,13 @@ void HHGate::updateTauMinf()
void HHGate::updateTables()
{
- if ( alpha_.size() == 0 || beta_.size() == 0 )
- return;
- vector< double > parms = alpha_;
- parms.insert( parms.end(), beta_.begin(), beta_.end() );
- parms.push_back( A_.size() );
- parms.push_back( xmin_ );
- parms.push_back( xmax_ );
+ if ( alpha_.size() == 0 || beta_.size() == 0 )
+ return;
+ vector< double > parms = alpha_;
+ parms.insert( parms.end(), beta_.begin(), beta_.end() );
+ parms.push_back( A_.size() );
+ parms.push_back( xmin_ );
+ parms.push_back( xmax_ );
- setupTables( parms, 0 );
+ setupTables( parms, 0 );
}
diff --git a/moose-core/biophysics/HHGate.h b/moose-core/biophysics/HHGate.h
index a5c79eb5dfcc68e65ef591c80df5b6fd91d97995..eadb2821cf1e3f293296723d4d7cec768dd76e54 100644
--- a/moose-core/biophysics/HHGate.h
+++ b/moose-core/biophysics/HHGate.h
@@ -28,6 +28,7 @@
* Field assignment to the HHGate should be possible only from the
* original HHChannel, but all the others do have read permission.
*/
+
class HHGate
{
friend void testHHGateLookup();
@@ -100,12 +101,10 @@ class HHGate
//////////////////////////////////////////////////////////
// DestFinfos
//////////////////////////////////////////////////////////
- void setupTau( const Eref& e,
- vector< double > parms );
+ void setupTau( const Eref& e, vector< double > parms );
void tweakAlpha();
void tweakTau();
- void setupGate( const Eref& e,
- vector< double > parms );
+ void setupGate( const Eref& e, vector< double > parms );
void setupTables( const vector< double >& parms, bool doTau );
void tweakTables( bool doTau );
diff --git a/moose-core/biophysics/Neuron.cpp b/moose-core/biophysics/Neuron.cpp
index 15ec8e60ec4b4ffcc82a852f3b3c5985ecc8d518..4d5993f1676aa1a4fe03ba6719563880115e8ee6 100644
--- a/moose-core/biophysics/Neuron.cpp
+++ b/moose-core/biophysics/Neuron.cpp
@@ -1141,10 +1141,29 @@ void Neuron::setChannelDistribution( const Eref& e, vector< string > v )
vector< vector< string > > lines;
if ( parseDistrib( lines, v ) )
{
+ unsigned int index = 0;
+ vector< unsigned int > chanIndices;
+ vector< unsigned int > temp;
channelDistribution_ = v;
+ // We need to ensure that Ca_concs are created before any channels
+ // since the channels may want to connect to them.
for ( unsigned int i = 0; i < lines.size(); ++i )
{
- vector< string >& temp = lines[i];
+ Id proto( "/library/" + lines[i][0] );
+ if ( proto != Id() ) {
+ if ( proto.element()->cinfo()->isA( "CaConcBase" ) ) {
+ chanIndices.push_back( i );
+ } else {
+ temp.push_back( i );
+ }
+ }
+ }
+ chanIndices.insert( chanIndices.end(), temp.begin(), temp.end() );
+ assert( chanIndices.size() == lines.size() );
+
+ for ( unsigned int i = 0; i < lines.size(); ++i )
+ {
+ vector< string >& temp = lines[chanIndices[i]];
vector< ObjId > elist;
vector< double > val;
buildElist( e, temp, elist, val );
diff --git a/moose-core/builtins/CMakeLists.txt b/moose-core/builtins/CMakeLists.txt
index 9c2260113e0160cec1e5f827f1d36f2bf3c3a17c..3df4cd964824591929dcd158f7c87b01564dd66e 100644
--- a/moose-core/builtins/CMakeLists.txt
+++ b/moose-core/builtins/CMakeLists.txt
@@ -19,6 +19,7 @@ set(SRCS
Stats.cpp
Interpol2D.cpp
SpikeStats.cpp
+ SocketStreamer.cpp
testBuiltins.cpp
)
diff --git a/moose-core/builtins/SocketStreamer.cpp b/moose-core/builtins/SocketStreamer.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..e3097f088bd2b7f99d52743a52ce249ff7d01141
--- /dev/null
+++ b/moose-core/builtins/SocketStreamer.cpp
@@ -0,0 +1,591 @@
+/***
+ * Filename: SocketStreamer.cpp
+ *
+ * Description: TCP and Unix Domain Socket to stream data.
+ *
+ * Author: Dilawar Singh <dilawar.s.rajput@gmail.com>
+ * Organization: NCBS Bangalore
+ *
+ * License: See MOOSE licence.
+ */
+
+#include <algorithm>
+#include <sstream>
+#include <chrono>
+#include <thread>
+#include <unistd.h>
+
+#include "../basecode/global.h"
+#include "../basecode/header.h"
+#include "../scheduling/Clock.h"
+#include "../utility/utility.h"
+#include "../shell/Shell.h"
+#include "SocketStreamer.h"
+
+const Cinfo* SocketStreamer::initCinfo()
+{
+ /*-----------------------------------------------------------------------------
+ * Finfos
+ *-----------------------------------------------------------------------------*/
+ static ValueFinfo< SocketStreamer, size_t > port(
+ "port"
+ , "Set port number for streaming. Valid only of TCP socket."
+ , &SocketStreamer::setPort
+ , &SocketStreamer::getPort
+ );
+
+ static ValueFinfo< SocketStreamer, string > address(
+ "address"
+ , "Set adresss for socket e.g. http://localhost:31416 (host:port for TCP SOCKET) "
+ ", or file:///tmp/MOOSE_SOCK for UNIX domain socket."
+ , &SocketStreamer::setAddress
+ , &SocketStreamer::getAddress
+ );
+
+ static ReadOnlyValueFinfo< SocketStreamer, size_t > numTables (
+ "numTables"
+ , "Number of Tables handled by SocketStreamer "
+ , &SocketStreamer::getNumTables
+ );
+
+ /*-----------------------------------------------------------------------------
+ *
+ *-----------------------------------------------------------------------------*/
+ static DestFinfo process(
+ "process"
+ , "Handle process call"
+ , new ProcOpFunc<SocketStreamer>(&SocketStreamer::process)
+ );
+
+ static DestFinfo reinit(
+ "reinit"
+ , "Handles reinit call"
+ , new ProcOpFunc<SocketStreamer> (&SocketStreamer::reinit)
+ );
+
+ static DestFinfo addTable(
+ "addTable"
+ , "Add a table to SocketStreamer"
+ , new OpFunc1<SocketStreamer, Id>(&SocketStreamer::addTable)
+ );
+
+ static DestFinfo addTables(
+ "addTables"
+ , "Add many tables to SocketStreamer"
+ , new OpFunc1<SocketStreamer, vector<Id> >(&SocketStreamer::addTables)
+ );
+
+ static DestFinfo removeTable(
+ "removeTable"
+ , "Remove a table from SocketStreamer"
+ , new OpFunc1<SocketStreamer, Id>(&SocketStreamer::removeTable)
+ );
+
+ static DestFinfo removeTables(
+ "removeTables"
+ , "Remove tables -- if found -- from SocketStreamer"
+ , new OpFunc1<SocketStreamer, vector<Id>>(&SocketStreamer::removeTables)
+ );
+
+ /*-----------------------------------------------------------------------------
+ * ShareMsg definitions.
+ *-----------------------------------------------------------------------------*/
+ static Finfo* procShared[] =
+ {
+ &process, &reinit, &addTable, &addTables, &removeTable, &removeTables
+ };
+
+ static SharedFinfo proc(
+ "proc",
+ "Shared message for process and reinit",
+ procShared, sizeof( procShared ) / sizeof( const Finfo* )
+ );
+
+ static Finfo * socketStreamFinfo[] =
+ {
+ &port, &address, &proc, &numTables
+ };
+
+ static string doc[] =
+ {
+ "Name", "SocketStreamer",
+ "Author", "Dilawar Singh (@dilawar, github), 2018",
+ "Description", "SocketStreamer: Stream moose.Table data to a socket.\n"
+ };
+
+ static Dinfo< SocketStreamer > dinfo;
+
+ static Cinfo tableStreamCinfo(
+ "SocketStreamer",
+ TableBase::initCinfo(),
+ socketStreamFinfo,
+ sizeof( socketStreamFinfo )/sizeof(Finfo *),
+ &dinfo,
+ doc,
+ sizeof(doc) / sizeof(string)
+ );
+
+ return &tableStreamCinfo;
+}
+
+static const Cinfo* tableStreamCinfo = SocketStreamer::initCinfo();
+
+// Constructor
+SocketStreamer::SocketStreamer() :
+ currTime_(0.0)
+ , numMaxClients_(1)
+ , sockType_ ( UNIX_DOMAIN_SOCKET )
+ , sockfd_(-1)
+ , clientfd_(-1)
+ , ip_( TCP_SOCKET_IP )
+ , port_( TCP_SOCKET_PORT )
+ , address_ ( "file://MOOSE" )
+{
+ clk_ = reinterpret_cast<Clock*>( Id(1).eref().data() );
+
+ // Not all compilers allow initialization during the declaration of class
+ // methods.
+ columns_.push_back( "time" ); /* First column is time. */
+ tables_.resize(0);
+ tableIds_.resize(0);
+ tableTick_.resize(0);
+ tableDt_.resize(0);
+
+}
+
+SocketStreamer& SocketStreamer::operator=( const SocketStreamer& st )
+{
+ return *this;
+}
+
+
+// Deconstructor
+SocketStreamer::~SocketStreamer()
+{
+ // Now cleanup the socket as well.
+ all_done_ = true;
+ if(sockfd_ > 0)
+ {
+ LOG(moose::debug, "Closing socket " << sockfd_ );
+ shutdown(sockfd_, SHUT_RD);
+ close(sockfd_);
+
+ if( sockType_ == UNIX_DOMAIN_SOCKET )
+ ::unlink( unixSocketFilePath_.c_str() );
+ }
+
+ if( processThread_.joinable() )
+ processThread_.join();
+}
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Stop a thread.
+ * See: http://www.bo-yang.net/2017/11/19/cpp-kill-detached-thread
+ *
+ * @Param tname name of thread.
+ */
+/* ----------------------------------------------------------------------------*/
+//void SocketStreamer::stopThread(const std::string& tname)
+//{
+// ThreadMap::const_iterator it = tm_.find(tname);
+// if (it != tm_.end())
+// {
+// it->second.std::thread::~thread(); // thread not killed
+// tm_.erase(tname);
+// LOG(moose::debug, "Thread " << tname << " killed." );
+// }
+//}
+
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Connect to a client. If already connected to one, then do not make
+ * any more connections.
+ */
+/* ----------------------------------------------------------------------------*/
+void SocketStreamer::listenToClients(size_t numMaxClients)
+{
+ assert(0 < sockfd_ );
+ assert( numMaxClients > 0 );
+ numMaxClients_ = numMaxClients;
+ if(-1 == listen(sockfd_, numMaxClients_))
+ LOG(moose::error, "Failed listen() on socket " << sockfd_
+ << ". Error was: " << strerror(errno) );
+
+}
+
+void SocketStreamer::initServer( void )
+{
+ setSocketType( );
+ if( sockType_ == UNIX_DOMAIN_SOCKET )
+ initUDSServer();
+ else
+ initTCPServer();
+
+ LOG(moose::debug, "Successfully created SocketStreamer server: " << sockfd_);
+
+ // Listen for incoming clients. This function does nothing if connection is
+ // already made.
+ listenToClients(2);
+}
+
+void SocketStreamer::configureSocketServer( )
+{
+ // One can set socket option using setsockopt function. See manual page
+ // for details. We are making it 'reusable'.
+ int on = 1;
+
+#ifdef SO_REUSEADDR
+ if(0 > setsockopt(sockfd_, SOL_SOCKET, SO_REUSEPORT, (const char *)&on, sizeof(on)))
+ LOG(moose::warning, "Warn: setsockopt() failed");
+#endif
+
+ if(0 > setsockopt(sockfd_, SOL_SOCKET, SO_REUSEADDR, (const char *)&on, sizeof(on)))
+ LOG(moose::warning, "Warn: setsockopt() failed");
+}
+
+void SocketStreamer::initUDSServer( void )
+{
+ // PF_UNIX means that sockets are local.
+ sockfd_ = socket(PF_UNIX, SOCK_STREAM, 0);
+ if( ! sockfd_)
+ {
+ isValid_ = false;
+ perror( "Socket" );
+ }
+
+ if( sockfd_ > 0 )
+ {
+ unixSocketFilePath_ = address_.substr(7); bzero(&sockAddrUDS_, sizeof(sockAddrUDS_));
+ sockAddrUDS_.sun_family = AF_UNIX;
+ strncpy(sockAddrUDS_.sun_path, unixSocketFilePath_.c_str(), sizeof(sockAddrUDS_.sun_path)-1);
+ configureSocketServer();
+
+ // Bind. Make sure bind is not std::bind
+ if(0 > ::bind(sockfd_, (struct sockaddr*) &sockAddrUDS_, sizeof(sockAddrUDS_)))
+ {
+ isValid_ = false;
+ LOG(moose::warning, "Warn: Failed to create socket at " << unixSocketFilePath_
+ << ". File descriptor: " << sockfd_
+ << ". Erorr: " << strerror(errno)
+ );
+ }
+ }
+
+ if( (! isValid_) || (sockfd_ < 0) )
+ ::unlink( unixSocketFilePath_.c_str() );
+}
+
+void SocketStreamer::initTCPServer( void )
+{
+ // Create a blocking socket.
+ LOG( moose::debug, "Creating TCP socket on port: " << port_ );
+ sockfd_ = socket(AF_INET, SOCK_STREAM, 0);
+ if( 0 > sockfd_ )
+ {
+ perror("socket");
+ isValid_ = false;
+ return;
+ }
+
+ configureSocketServer();
+ bzero((char*) &sockAddrTCP_, sizeof(sockAddrTCP_));
+ sockAddrTCP_.sin_family = AF_INET;
+ sockAddrTCP_.sin_addr.s_addr = INADDR_ANY;
+ sockAddrTCP_.sin_port = htons( port_ );
+
+ // Bind. Make sure bind is not std::bind
+ if(0 > ::bind(sockfd_, (struct sockaddr*) &sockAddrTCP_, sizeof(sockAddrTCP_)))
+ {
+ isValid_ = false;
+ LOG(moose::warning, "Warn: Failed to create server at " << ip_ << ":" << port_
+ << ". File descriptor: " << sockfd_
+ << ". Erorr: " << strerror(errno)
+ );
+ return;
+ }
+}
+
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Stream data over socket.
+ *
+ * @Returns True of success, false otherwise. It is callee job to clean up data_
+ * on a successful return from this function.
+ */
+/* ----------------------------------------------------------------------------*/
+bool SocketStreamer::streamData( )
+{
+ if( clientfd_ > 0)
+ {
+ buffer_ += dataToString();
+
+ if( buffer_.size() < frameSize_ )
+ buffer_ += string(frameSize_-buffer_.size(), ' ');
+
+ string toSend = buffer_.substr(0, frameSize_);
+
+ int sent = send(clientfd_, buffer_.substr(0, frameSize_).c_str(), frameSize_, MSG_MORE);
+ buffer_ = buffer_.erase(0, sent);
+
+ assert( sent == (int)frameSize_);
+ LOG(moose::debug, "Sent " << sent << " bytes." );
+
+ if(0 > sent)
+ {
+ LOG(moose::warning, "Failed to send. Error: " << strerror(errno)
+ << ". client id: " << clientfd_ );
+ return false;
+ }
+
+ // clear up the tables.
+ for( auto t : tables_ )
+ t->clearVec();
+ return true;
+ }
+ else
+ LOG(moose::warning, "No client found to stream data. ClientFD: " << clientfd_ );
+
+ return false;
+}
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Convert table to string (use scientific notation).
+ *
+ * @Returns String in JSON like format.
+ */
+/* ----------------------------------------------------------------------------*/
+string SocketStreamer::dataToString( )
+{
+ stringstream ss;
+ // Enabling this would be require quite a lot of characters to be streamed.
+ //ss.precision( 7 );
+ //ss << std::scientific;
+ vector<double> data;
+
+ // Else stream the data.
+ ss << "{";
+ for( size_t i = 0; i < tables_.size(); i++)
+ {
+ ss << "\"" << columns_[i+1] << "\":[";
+ ss << tables_[i]->toJSON(true);
+ ss << "],";
+ }
+
+ // remove , at the end else it won't be a valid JSON.
+ string res = ss.str();
+ if( ',' == res.back())
+ res.pop_back();
+ res += "}\n";
+ return res;
+}
+
+bool SocketStreamer::enoughDataToStream(size_t minsize)
+{
+ for( size_t i = 0; i < tables_.size(); i++)
+ if(tables_[i]->getVec().size() >= minsize )
+ return true;
+ return false;
+}
+
+void SocketStreamer::connectAndStream( )
+{
+ currTime_ = clk_->getCurrentTime();
+
+ // If server was invalid then there is no point.
+ if( ! isValid_ )
+ {
+ LOG( moose::error, "Server could not set up." );
+ return;
+ }
+
+ // Now lets get into a loop to stream data.
+ while( (! all_done_) )
+ {
+ clientfd_ = ::accept(sockfd_, NULL, NULL);
+ if( clientfd_ >= 0 )
+ streamData();
+ }
+}
+
+/**
+ * @brief Reinit. We make sure it is non-blocking.
+ *
+ * @param e
+ * @param p
+ */
+void SocketStreamer::reinit(const Eref& e, ProcPtr p)
+{
+ if( tables_.size() == 0 )
+ {
+ moose::showWarn( "No table found. Disabling SocketStreamer.\nDid you forget"
+ " to call addTables() on SocketStreamer object. " + e.objId().path()
+ );
+ e.element()->setTick( -2 ); /* Disable process */
+ return;
+ }
+
+ thisDt_ = clk_->getTickDt( e.element()->getTick() );
+
+ // Push each table dt_ into vector of dt
+ for( size_t i = 0; i < tables_.size(); i++)
+ {
+ Id tId = tableIds_[i];
+ int tickNum = tId.element()->getTick();
+ tableDt_.push_back( clk_->getTickDt( tickNum ) );
+ }
+
+ // This should only be called once.
+ initServer();
+
+ // Launch a thread in background which monitors the any client trying to
+ // make connection to server.
+ processThread_ = std::thread(&SocketStreamer::connectAndStream, this);
+}
+
+/**
+ * @brief This function is called at its clock tick.
+ *
+ * @param e
+ * @param p
+ */
+void SocketStreamer::process(const Eref& e, ProcPtr p)
+{
+ // It does nothing. See the connectAndStream function.
+ ;
+}
+
+/**
+ * @brief Add a table to streamer.
+ *
+ * @param table Id of table.
+ */
+void SocketStreamer::addTable( Id table )
+{
+ // If this table is not already in the vector, add it.
+ for( size_t i = 0; i < tableIds_.size(); i++)
+ if( table.path() == tableIds_[i].path() )
+ 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() );
+
+ // NOTE: If user can make sure that names are unique in table, using name is
+ // better than using the full path.
+ if( t->getColumnName().size() > 0 )
+ columns_.push_back( t->getColumnName( ) );
+ else
+ columns_.push_back( moose::moosePathToUserPath( table.path() ) );
+}
+
+/**
+ * @brief Add multiple tables to SocketStreamer.
+ *
+ * @param tables
+ */
+void SocketStreamer::addTables( vector<Id> tables )
+{
+ if( tables.size() == 0 )
+ return;
+ for( vector<Id>::const_iterator it = tables.begin(); it != tables.end(); it++)
+ addTable( *it );
+}
+
+void SocketStreamer::addTables( vector<ObjId> tables )
+{
+ if( tables.size() == 0 )
+ return;
+ for( auto t : tables )
+ addTable( Id(t) );
+}
+
+
+/**
+ * @brief Remove a table from SocketStreamer.
+ *
+ * @param table. Id of table.
+ */
+void SocketStreamer::removeTable( Id table )
+{
+ int matchIndex = -1;
+ for (size_t i = 0; i < tableIds_.size(); i++)
+ {
+ if( table.path() == tableIds_[i].path() )
+ {
+ matchIndex = i;
+ break;
+ }
+ }
+
+ if( matchIndex > -1 )
+ {
+ tableIds_.erase( tableIds_.begin() + matchIndex );
+ tables_.erase( tables_.begin() + matchIndex );
+ columns_.erase( columns_.begin() + matchIndex );
+ }
+}
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Determines socket type from the given address.
+ */
+/* ----------------------------------------------------------------------------*/
+void SocketStreamer::setSocketType( )
+{
+ LOG( moose::debug, "Socket address is " << address_ );
+ if( "file://" == address_.substr(0, 7))
+ sockType_ = UNIX_DOMAIN_SOCKET;
+ else if( "http://" == address_.substr(0,7))
+ sockType_ = TCP_SOCKET;
+ else
+ sockType_ = UNIX_DOMAIN_SOCKET;
+ return;
+}
+
+/**
+ * @brief Remove multiple tables -- if found -- from SocketStreamer.
+ *
+ * @param tables
+ */
+void SocketStreamer::removeTables( vector<Id> tables )
+{
+ for( vector<Id>::const_iterator it = tables.begin(); it != tables.end(); it++)
+ removeTable( *it );
+}
+
+/**
+ * @brief Get the number of tables handled by SocketStreamer.
+ *
+ * @return Number of tables.
+ */
+size_t SocketStreamer::getNumTables( void ) const
+{
+ return tables_.size();
+}
+
+
+void SocketStreamer::setPort( const size_t port )
+{
+ port_ = port;
+}
+
+size_t SocketStreamer::getPort( void ) const
+{
+ assert( port_ > 1 );
+ return port_;
+}
+
+void SocketStreamer::setAddress( const string addr )
+{
+ address_ = addr;
+}
+
+string SocketStreamer::getAddress( void ) const
+{
+ return address_;
+}
diff --git a/moose-core/builtins/SocketStreamer.h b/moose-core/builtins/SocketStreamer.h
new file mode 100644
index 0000000000000000000000000000000000000000..c52bb7dd4d1419895d16d7ba3f9ddc9cb331fa45
--- /dev/null
+++ b/moose-core/builtins/SocketStreamer.h
@@ -0,0 +1,164 @@
+/***
+ * Stream table data to a TCP socket.
+ */
+
+#ifndef SocketStreamer_INC
+#define SocketStreamer_INC
+
+#define STRINGSTREAM_DOUBLE_PRECISION 10
+
+#include <iostream>
+#include <string>
+#include <map>
+#include <fstream>
+#include <sstream>
+#include <thread>
+#include <atomic>
+
+#include "StreamerBase.h"
+#include "Table.h"
+
+// If cmake does not set it, use the default port.
+#ifndef TCP_SOCKET_PORT
+#define TCP_SOCKET_PORT 31416
+#endif
+
+#ifndef TCP_SOCKET_IP
+#define TCP_SOCKET_IP "127.0.0.1"
+#endif
+
+// Before send() can be used with c++.
+#define _XOPEN_SOURCE_EXTENDED 1
+
+// cmake should set include path.
+#include <sys/socket.h>
+#include <sys/poll.h>
+#include <sys/types.h>
+#include <sys/ioctl.h>
+#include <sys/un.h>
+#include <netinet/in.h>
+
+// MSG_MORE is not defined in OSX. So stupid!
+#ifndef MSG_MORE
+#define MSG_MORE 0
+#endif
+
+using namespace std;
+
+typedef enum t_socket_type_ {TCP_SOCKET, UNIX_DOMAIN_SOCKET} SocketType; // Type of socket.
+
+class Clock;
+
+class SocketStreamer : public StreamerBase
+{
+
+public:
+ SocketStreamer();
+ ~SocketStreamer();
+
+ SocketStreamer& operator=( const SocketStreamer& st );
+
+ string getFormat( void ) const;
+ void setFormat( string format );
+
+ /*-----------------------------------------------------------------------------
+ * Socket Server
+ *-----------------------------------------------------------------------------*/
+ // Initialize server.
+ void initServer( void );
+ void initTCPServer( void );
+ void initUDSServer( void );
+
+ /* common configuration options */
+ void configureSocketServer( void );
+
+ // Make connection to client
+ void listenToClients(size_t numMaxClients);
+
+ /* Cleaup before quitting */
+ void cleanUp( void );
+
+ string getAddress( void ) const;
+ void setAddress( const string addr );
+
+ size_t getPort( void ) const;
+ void setPort( const size_t port );
+
+ SocketType getSocketType( );
+ void setSocketType(void);
+
+ /*-----------------------------------------------------------------------------
+ * Streaming data.
+ *-----------------------------------------------------------------------------*/
+ bool enoughDataToStream(size_t minsize=10);
+ bool streamData();
+ void connectAndStream( );
+
+ size_t getNumTables( void ) const;
+
+ void addTable( Id table );
+ void addTables( vector<Id> tables);
+ void addTables( vector<ObjId> tables);
+
+ void removeTable( Id table );
+ void removeTables( vector<Id> table );
+
+ string dataToString();
+
+ // void stopThread(const std::string& tname);
+
+ /** Dest functions.
+ * The process function called by scheduler on every tick
+ */
+ void process(const Eref& e, ProcPtr p);
+
+ /**
+ * The reinit function called by scheduler for the reset
+ */
+ void reinit(const Eref& e, ProcPtr p);
+
+ static const Cinfo * initCinfo();
+
+private:
+
+ // dt_ and tick number of Table's clock
+ vector<double> tableDt_;
+ vector<unsigned int> tableTick_;
+ double currTime_;
+
+ // Used for adding or removing tables
+ vector<Id> tableIds_;
+ vector<Table*> tables_;
+ vector<string> columns_;
+
+ /* Socket related */
+ int numMaxClients_;
+ SocketType sockType_ = UNIX_DOMAIN_SOCKET; // Default is UNIX_DOMAIN_SOCKET
+ int sockfd_; // socket file descriptor.
+ int clientfd_; // client file descriptor
+
+ // TCP socket.
+ string ip_; // ip_ address of server.
+ unsigned short port_; // port number if socket is TCP_SOCKET
+ string address_; // adress of socket. Specified by user.
+ string unixSocketFilePath_;
+
+ // address holdder for TCP and UDS sockets.
+ struct sockaddr_in sockAddrTCP_;
+ struct sockaddr_un sockAddrUDS_;
+
+ /* For data handling */
+ bool all_done_ = false;
+ bool isValid_ = true;
+ std::thread processThread_;
+ string buffer_;
+ double thisDt_;
+
+ size_t frameSize_ = 2048;
+
+ // We need clk_ pointer for handling
+ Clock* clk_ = nullptr;
+
+};
+
+#endif /* ----- #ifndef SocketStreamer_INC ----- */
diff --git a/moose-core/builtins/Streamer.cpp b/moose-core/builtins/Streamer.cpp
index 5ecde62108ae1d59ee861868eedd83818ae4275e..c583be1fee2ee8cc00ec68c1f6ee8e4cef2a4293 100644
--- a/moose-core/builtins/Streamer.cpp
+++ b/moose-core/builtins/Streamer.cpp
@@ -201,7 +201,7 @@ void Streamer::reinit(const Eref& e, ProcPtr p)
{
Id tId = tableIds_[i];
int tickNum = tId.element()->getTick();
- tableDt_.push_back( clk->getTickDt( tickNum ) );
+ tableDt_.push_back( clk->getTickDt(tickNum) );
}
// Make sure all tables have same dt_ else disable the streamer.
diff --git a/moose-core/builtins/StreamerBase.cpp b/moose-core/builtins/StreamerBase.cpp
index cb436b99a6926110b2f5a6073a801de40e5e705c..e6d590be0fe1b2a06a2c242946e4814a32a8ec38 100644
--- a/moose-core/builtins/StreamerBase.cpp
+++ b/moose-core/builtins/StreamerBase.cpp
@@ -78,7 +78,6 @@ void StreamerBase::writeToOutFile( const string& filepath
}
}
-
/* Write to a csv file. */
void StreamerBase::writeToCSVFile( const string& filepath, const string& openmode
, const vector<double>& data, const vector<string>& columns )
@@ -123,3 +122,10 @@ void StreamerBase::writeToNPYFile( const string& filepath, const string& openmod
cnpy2::save_numpy<double>( filepath, data, columns, openmode );
}
+string StreamerBase::vectorToCSV( const vector<double>& ys, const string& fmt )
+{
+ stringstream ss;
+ for( auto v : ys )
+ ss << v << ",";
+ return ss.str();
+}
diff --git a/moose-core/builtins/StreamerBase.h b/moose-core/builtins/StreamerBase.h
index c23dd5001c59b9a13b6f8852a5a14330386ac4df..b3e035b1ae2b87663d64cbba9196e5c3be997ed9 100644
--- a/moose-core/builtins/StreamerBase.h
+++ b/moose-core/builtins/StreamerBase.h
@@ -86,6 +86,17 @@ public:
);
+ /* --------------------------------------------------------------------------*/
+ /**
+ * @Synopsis Return a csv representation of a vector.
+ *
+ * @Param ys vector of double.
+ *
+ * @Returns CSV string.
+ */
+ /* ----------------------------------------------------------------------------*/
+ string vectorToCSV( const vector<double>& ys, const string& fmt );
+
private:
string outfilePath_;
diff --git a/moose-core/builtins/Table.cpp b/moose-core/builtins/Table.cpp
index f5a6b7710e336958109d44dfb1e51d7e4ff724fd..4f426b148e09428928a75bb2569bf04c0c2263cd 100644
--- a/moose-core/builtins/Table.cpp
+++ b/moose-core/builtins/Table.cpp
@@ -210,12 +210,12 @@ const Cinfo* Table::initCinfo()
static const Cinfo* tableCinfo = Table::initCinfo();
-Table::Table() :
- threshold_( 0.0 ) ,
- lastTime_( 0.0 ) ,
- input_( 0.0 ),
- fired_(false),
- useSpikeMode_(false),
+Table::Table() :
+ threshold_( 0.0 ) ,
+ lastTime_( 0.0 ) ,
+ input_( 0.0 ),
+ fired_(false),
+ useSpikeMode_(false),
dt_( 0.0 )
{
// Initialize the directory to which each table should stream.
@@ -230,10 +230,9 @@ Table::~Table( )
// Make sure to write to rest of the entries to file before closing down.
if( useStreamer_ )
{
- zipWithTime( vec(), data_, lastTime_ );
+ mergeWithTime( data_ );
StreamerBase::writeToOutFile( outfile_, format_, "a", data_, columns_ );
- clearVec();
- data_.clear();
+ clearAllVecs();
}
}
@@ -250,17 +249,19 @@ Table& Table::operator=( const Table& tab )
void Table::process( const Eref& e, ProcPtr p )
{
lastTime_ = p->currTime;
+ tvec_.push_back(lastTime_);
// Copy incoming data to ret and insert into vector.
vector< double > ret;
requestOut()->send( e, &ret );
- if (useSpikeMode_) {
- for ( vector< double >::const_iterator
- i = ret.begin(); i != ret.end(); ++i )
- spike( *i );
- } else {
- vec().insert( vec().end(), ret.begin(), ret.end() );
- }
+
+ if (useSpikeMode_)
+ {
+ for ( vector< double >::const_iterator i = ret.begin(); i != ret.end(); ++i )
+ spike( *i );
+ }
+ else
+ vec().insert( vec().end(), ret.begin(), ret.end() );
/* If we are streaming to a file, let's write to a file. And clean the
* vector.
@@ -270,14 +271,20 @@ void Table::process( const Eref& e, ProcPtr p )
{
if( fmod(lastTime_, 5.0) == 0.0 or getVecSize() >= 10000 )
{
- zipWithTime( vec(), data_, lastTime_ );
+ mergeWithTime( data_ );
StreamerBase::writeToOutFile( outfile_, format_ , "a", data_, columns_ );
- data_.clear();
- clearVec();
+ clearAllVecs();
}
}
}
+void Table::clearAllVecs()
+{
+ clearVec();
+ tvec_.clear();
+ data_.clear();
+}
+
/**
* @brief Reinitialize
*
@@ -313,21 +320,22 @@ void Table::reinit( const Eref& e, ProcPtr p )
lastTime_ = 0;
vector< double > ret;
requestOut()->send( e, &ret );
- if (useSpikeMode_) {
- for ( vector< double >::const_iterator
- i = ret.begin(); i != ret.end(); ++i )
- spike( *i );
- } else {
- vec().insert( vec().end(), ret.begin(), ret.end() );
- }
+
+ if (useSpikeMode_)
+ {
+ for (vector<double>::const_iterator i = ret.begin(); i != ret.end(); ++i )
+ spike( *i );
+ }
+ else
+ vec().insert( vec().end(), ret.begin(), ret.end() );
+
+ tvec_.push_back(lastTime_);
if( useStreamer_ )
{
- zipWithTime( vec(), data_, lastTime_ );
+ mergeWithTime( data_ );
StreamerBase::writeToOutFile( outfile_, format_, "w", data_, columns_);
- clearVec();
- data_.clear();
- clearVec();
+ clearAllVecs();
}
}
@@ -342,15 +350,20 @@ void Table::input( double v )
void Table::spike( double v )
{
- if ( fired_ ) { // Wait for it to go below threshold
- if ( v < threshold_ )
- fired_ = false;
- } else {
- if ( v > threshold_ ) { // wait for it to go above threshold.
- fired_ = true;
- vec().push_back( lastTime_ );
- }
- }
+ if ( fired_ )
+ { // Wait for it to go below threshold
+ if ( v < threshold_ )
+ fired_ = false;
+ }
+ else
+ {
+ if ( v > threshold_ )
+ {
+ // wait for it to go above threshold.
+ fired_ = true;
+ vec().push_back( lastTime_ );
+ }
+ }
}
//////////////////////////////////////////////////////////////
@@ -450,15 +463,39 @@ double Table::getDt( void ) const
* @brief Take the vector from table and timestamp it. It must only be called
* when packing the data for writing.
*/
-void Table::zipWithTime( const vector<double>& v
- , vector<double>& tvec
- , const double& currTime
- )
+void Table::mergeWithTime( vector<double>& data )
+{
+ auto v = vec();
+ for (size_t i = 0; i < v.size(); i++)
+ {
+ data.push_back(tvec_[i]);
+ data.push_back(v[i]);
+ }
+}
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis. Convert table data to JOSN.
+ *
+ * @Param t. Upto this time.
+ * @Param withTime. Zip with time.
+ *
+ * @Returns string.
+ */
+/* ----------------------------------------------------------------------------*/
+string Table::toJSON( bool withTime)
{
- size_t N = v.size();
- for (size_t i = 0; i < N; i++)
+ auto v = vec();
+ stringstream ss;
+ for (size_t i = 0; i < v.size(); i++)
{
- tvec.push_back( currTime - (N - i - 1 ) * dt_ );
- tvec.push_back( v[i] );
+ if(withTime)
+ ss << '[' << tvec_[i] << ',' << v[i] << "],";
+ else
+ ss << v[i] << ',';
}
+ string res = ss.str();
+ if( ',' == res.back())
+ res.pop_back();
+ return res;
}
diff --git a/moose-core/builtins/Table.h b/moose-core/builtins/Table.h
index 34397cde40e0056b5a57517d54831db73cbc9b52..b3a0293bf7796fec8e568063f1e6e2f1e59a09c2 100644
--- a/moose-core/builtins/Table.h
+++ b/moose-core/builtins/Table.h
@@ -48,11 +48,12 @@ public:
// Access the dt_ of table.
double getDt ( void ) const;
- void zipWithTime (
- const vector<double>& yvec
- , vector<double>& tvec
- , const double& lasttime
- );
+ // merge time value among values. e.g. t1, v1, t2, v2, etc.
+ void mergeWithTime( vector<double>& data );
+
+ string toJSON(bool withTime=true);
+
+ void clearAllVecs();
//////////////////////////////////////////////////////////////////
// Dest funcs
@@ -71,17 +72,15 @@ public:
static const Cinfo* initCinfo();
private:
+
double threshold_;
double lastTime_;
double input_;
- bool fired_;
- bool useSpikeMode_;
+ bool fired_;
+ bool useSpikeMode_;
- /**
- * @brief Keep the data, each entry is preceeded by time value.
- * t0, v0, t1, v1, t2, v2 etc.
- */
vector<double> data_;
+ vector<double> tvec_; /* time data */
vector<string> columns_; /* Store the name of tables */
string tablePath_;
diff --git a/moose-core/builtins/TableBase.cpp b/moose-core/builtins/TableBase.cpp
index e4467c6f0be8b4f70e169ce2457fa05d14b04e9a..c0976bc2de0d12032059c34bbdf2ab7c5bed270a 100644
--- a/moose-core/builtins/TableBase.cpp
+++ b/moose-core/builtins/TableBase.cpp
@@ -14,139 +14,143 @@
const Cinfo* TableBase::initCinfo()
{
- //////////////////////////////////////////////////////////////
- // Field Definitions
- //////////////////////////////////////////////////////////////
- static ValueFinfo< TableBase, vector< double > > vec(
- "vector",
- "vector with all table entries",
- &TableBase::setVec,
- &TableBase::getVec
- );
-
- static ValueFinfo< TableBase, string > plotDump(
- "plotDump",
- "'File plotname' for dumpling an xplot, as a workaround for an error in the xplot python interface. Note separator is a space. The return value is a dummy.",
- &TableBase::setPlotDump,
- &TableBase::getPlotDump
- );
-
- static ReadOnlyValueFinfo< TableBase, double > outputValue(
- "outputValue",
- "Output value holding current table entry or output of a calculation",
- &TableBase::getOutputValue
- );
-
- static ReadOnlyValueFinfo< TableBase, unsigned int > size(
- "size",
- "size of table. Note that this is the number of x divisions +1"
- "since it must represent the largest value as well as the"
- "smallest",
- &TableBase::getVecSize
- );
-
- static ReadOnlyLookupValueFinfo< TableBase, unsigned int, double > y(
- "y",
- "Value of table at specified index",
- &TableBase::getY
- );
-
- //////////////////////////////////////////////////////////////
- // MsgDest Definitions
- //////////////////////////////////////////////////////////////
-
- static DestFinfo linearTransform( "linearTransform",
- "Linearly scales and offsets data. Scale first, then offset.",
- new OpFunc2< TableBase, double, double >( &TableBase::linearTransform ) );
-
- static DestFinfo xplot( "xplot",
- "Dumps table contents to xplot-format file. "
- "Argument 1 is filename, argument 2 is plotname",
- new OpFunc2< TableBase, string, string >( &TableBase::xplot ) );
-
- static DestFinfo plainPlot( "plainPlot",
- "Dumps table contents to single-column ascii file. "
- "Uses scientific notation. "
- "Argument 1 is filename",
- new OpFunc1< TableBase, string >( &TableBase::plainPlot ) );
-
- static DestFinfo loadCSV( "loadCSV",
- "Reads a single column from a CSV file. "
- "Arguments: filename, column#, starting row#, separator",
- new OpFunc4< TableBase, string, int, int, char >(
- &TableBase::loadCSV ) );
-
- static DestFinfo loadXplot( "loadXplot",
- "Reads a single plot from an xplot file. "
- "Arguments: filename, plotname"
- "When the file has 2 columns, the 2nd column is loaded.",
- new OpFunc2< TableBase, string, string >(
- &TableBase::loadXplot ) );
-
- static DestFinfo loadXplotRange( "loadXplotRange",
- "Reads a single plot from an xplot file, and selects a "
- "subset of points from it. "
- "Arguments: filename, plotname, startindex, endindex"
- "Uses C convention: startindex included, endindex not included."
- "When the file has 2 columns, the 2nd column is loaded.",
- new OpFunc4< TableBase, string, string, unsigned int, unsigned int >(
- &TableBase::loadXplotRange ) );
-
- static DestFinfo compareXplot( "compareXplot",
- "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_operation"
- "Operations: rmsd (for RMSDifference), rmsr (RMSratio ), "
- "dotp (Dot product, not yet implemented).",
- new OpFunc3< TableBase, string, string, string >(
- &TableBase::compareXplot ) );
-
- static DestFinfo compareVec( "compareVec",
- "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_operation"
- "Operations: rmsd (for RMSDifference), rmsr (RMSratio ), "
- "dotp (Dot product, not yet implemented).",
- new OpFunc2< TableBase, vector< double >, string >(
- &TableBase::compareVec ) );
-
- static DestFinfo clearVec(
- "clearVec",
- "Handles request to clear the data vector",
- new OpFunc0< TableBase > (&TableBase::clearVec));
-
-
- static Finfo* tableBaseFinfos[] = {
- &vec, // Value
- &plotDump, // Value, used for debugging xplot function.
- &outputValue, // ReadOnlyValue
- &size, // ReadOnlyValue
- &y, // ReadOnlyLookupValue
- &linearTransform, // DestFinfo
- &xplot, // DestFinfo
- &plainPlot, // DestFinfo
- &loadCSV, // DestFinfo
- &loadXplot, // DestFinfo
- &loadXplotRange, // DestFinfo
- &compareXplot, // DestFinfo
- &compareVec, // DestFinfo
- &clearVec,
- };
-
- static Dinfo< TableBase > dinfo;
- static Cinfo tableCinfo (
- "TableBase",
- Neutral::initCinfo(),
- tableBaseFinfos,
- sizeof( tableBaseFinfos ) / sizeof ( Finfo* ),
- &dinfo
- );
-
- return &tableCinfo;
+ //////////////////////////////////////////////////////////////
+ // Field Definitions
+ //////////////////////////////////////////////////////////////
+ static ValueFinfo< TableBase, vector< double > > vec(
+ "vector",
+ "vector with all table entries",
+ &TableBase::setVec,
+ &TableBase::getVec
+ );
+
+ static ValueFinfo< TableBase, string > plotDump(
+ "plotDump",
+ "'File plotname' for dumpling an xplot, as a workaround for an error "
+ " in the xplot python interface. Note separator is a space. The return "
+ "value is a dummy.",
+ &TableBase::setPlotDump,
+ &TableBase::getPlotDump
+ );
+
+ static ReadOnlyValueFinfo< TableBase, double > outputValue(
+ "outputValue",
+ "Output value holding current table entry or output of a calculation",
+ &TableBase::getOutputValue
+ );
+
+ static ReadOnlyValueFinfo< TableBase, unsigned int > size(
+ "size",
+ "size of table. Note that this is the number of x divisions +1"
+ "since it must represent the largest value as well as the"
+ "smallest",
+ &TableBase::getVecSize
+ );
+
+ static ReadOnlyLookupValueFinfo< TableBase, unsigned int, double > y(
+ "y",
+ "Value of table at specified index",
+ &TableBase::getY
+ );
+
+ //////////////////////////////////////////////////////////////
+ // MsgDest Definitions
+ //////////////////////////////////////////////////////////////
+
+ static DestFinfo linearTransform( "linearTransform",
+ "Linearly scales and offsets data. Scale first, then offset.",
+ new OpFunc2< TableBase
+ , double
+ , double >(&TableBase::linearTransform ) );
+
+ static DestFinfo xplot( "xplot",
+ "Dumps table contents to xplot-format file. "
+ "Argument 1 is filename, argument 2 is plotname",
+ new OpFunc2< TableBase, string, string >( &TableBase::xplot ) );
+
+ static DestFinfo plainPlot( "plainPlot",
+ "Dumps table contents to single-column ascii file. "
+ "Uses scientific notation. "
+ "Argument 1 is filename",
+ new OpFunc1< TableBase, string >( &TableBase::plainPlot ) );
+
+ static DestFinfo loadCSV( "loadCSV",
+ "Reads a single column from a CSV file. "
+ "Arguments: filename, column#, starting row#, separator",
+ new OpFunc4< TableBase, string, int, int, char >(&TableBase::loadCSV ) );
+
+ static DestFinfo loadXplot( "loadXplot",
+ "Reads a single plot from an xplot file. "
+ "Arguments: filename, plotname"
+ "When the file has 2 columns, the 2nd column is loaded.",
+ new OpFunc2< TableBase, string, string >(
+ &TableBase::loadXplot ) );
+
+ static DestFinfo loadXplotRange( "loadXplotRange",
+ "Reads a single plot from an xplot file, and selects a "
+ "subset of points from it. "
+ "Arguments: filename, plotname, startindex, endindex"
+ "Uses C convention: startindex included, endindex not included."
+ "When the file has 2 columns, the 2nd column is loaded.",
+ new OpFunc4< TableBase, string, string, unsigned int, unsigned int >(
+ &TableBase::loadXplotRange ) );
+
+ static DestFinfo compareXplot( "compareXplot",
+ "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_operation"
+ "Operations: rmsd (for RMSDifference), rmsr (RMSratio ), "
+ "dotp (Dot product, not yet implemented).",
+ new OpFunc3< TableBase, string, string, string >(
+ &TableBase::compareXplot ) );
+
+ static DestFinfo compareVec( "compareVec",
+ "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_operation"
+ "Operations: rmsd (for RMSDifference), rmsr (RMSratio ), "
+ "dotp (Dot product, not yet implemented).",
+ new OpFunc2< TableBase, vector< double >, string >(
+ &TableBase::compareVec ) );
+
+ static DestFinfo clearVec(
+ "clearVec",
+ "Handles request to clear the data vector",
+ new OpFunc0< TableBase > (&TableBase::clearVec));
+
+
+ static Finfo* tableBaseFinfos[] =
+ {
+ &vec, // Value
+ &plotDump, // Value, used for debugging xplot function.
+ &outputValue, // ReadOnlyValue
+ &size, // ReadOnlyValue
+ &y, // ReadOnlyLookupValue
+ &linearTransform, // DestFinfo
+ &xplot, // DestFinfo
+ &plainPlot, // DestFinfo
+ &loadCSV, // DestFinfo
+ &loadXplot, // DestFinfo
+ &loadXplotRange, // DestFinfo
+ &compareXplot, // DestFinfo
+ &compareVec, // DestFinfo
+ &clearVec,
+ };
+
+ static Dinfo< TableBase > dinfo;
+ static Cinfo tableCinfo (
+ "TableBase",
+ Neutral::initCinfo(),
+ tableBaseFinfos,
+ sizeof( tableBaseFinfos ) / sizeof ( Finfo* ),
+ &dinfo
+ );
+
+ return &tableCinfo;
}
//////////////////////////////////////////////////////////////
@@ -171,42 +175,44 @@ void TableBase::linearTransform( double scale, double offset )
void TableBase::plainPlot( string fname )
{
- ofstream fout( fname.c_str(), ios_base::out );
- fout.precision( 18 );
- fout.setf( ios::scientific, ios::floatfield );
- for ( vector< double >::iterator i = vec_.begin(); i != vec_.end(); ++i)
- fout << *i << endl;
- fout << "\n";
+ ofstream fout( fname.c_str(), ios_base::out );
+ fout.precision( 18 );
+ fout.setf( ios::scientific, ios::floatfield );
+ for ( vector< double >::iterator i = vec_.begin(); i != vec_.end(); ++i)
+ fout << *i << endl;
+ fout << "\n";
}
void TableBase::xplot( string fname, string plotname )
{
- ofstream fout( fname.c_str(), ios_base::app );
- fout << "/newplot\n";
- fout << "/plotname " << plotname << "\n";
- for ( vector< double >::iterator i = vec_.begin(); i != vec_.end(); ++i)
- fout << *i << endl;
- fout << "\n";
+ ofstream fout( fname.c_str(), ios_base::app );
+ fout << "/newplot\n";
+ fout << "/plotname " << plotname << "\n";
+ for ( vector< double >::iterator i = vec_.begin(); i != vec_.end(); ++i)
+ fout << *i << endl;
+ fout << "\n";
}
bool isNamedPlot( const string& line, const string& plotname )
{
- static const unsigned int len = strlen( "/plotname" ) ;
- if ( line.size() < len + 2 )
- return 0;
- if ( line[0] == '/' && line[1] == 'p' ) {
- string name = line.substr( strlen( "/plotname" ) );
- string::size_type pos = name.find_first_not_of( " " );
- if ( pos == string::npos ) {
- cout << "TableBase::loadXplot: Malformed plotname line '" <<
- line << "'\n";
- return 0;
- }
- name = name.substr( pos );
- if ( plotname == name )
- return 1;
- }
- return 0;
+ static const unsigned int len = strlen( "/plotname" ) ;
+ if ( line.size() < len + 2 )
+ return 0;
+ if ( line[0] == '/' && line[1] == 'p' )
+ {
+ string name = line.substr( strlen( "/plotname" ) );
+ string::size_type pos = name.find_first_not_of( " " );
+ if ( pos == string::npos )
+ {
+ cout << "TableBase::loadXplot: Malformed plotname line '" <<
+ line << "'\n";
+ return 0;
+ }
+ name = name.substr( pos );
+ if ( plotname == name )
+ return 1;
+ }
+ return 0;
}
/*
@@ -230,190 +236,212 @@ bool lineHasExactlyTwoNumericalColumns( const string& line )
double getYcolumn( const string& line )
{
- istringstream sstream( line );
- double y1 = 0.0;
- double y2;
- double y3;
-
- if ( sstream >> y1 ) {
- if ( sstream >> y2 ) {
- if ( sstream >> y3 ) {
- return y1;
- } else {
- return y2;
- }
- }
- }
- return y1;
+ istringstream sstream( line );
+ double y1 = 0.0;
+ double y2;
+ double y3;
+
+ if ( sstream >> y1 )
+ {
+ if ( sstream >> y2 )
+ {
+ if ( sstream >> y3 )
+ {
+ return y1;
+ }
+ else
+ {
+ return y2;
+ }
+ }
+ }
+ return y1;
}
bool innerLoadXplot( string fname, string plotname, vector< double >& v )
{
- ifstream fin( fname.c_str() );
- if ( !fin.good() ) {
- cout << "TableBase::innerLoadXplot: Failed to open file " << fname <<endl;
- return 0;
- }
-
- string line;
- // Here we advance to the first numerical line.
- if ( plotname == "" ) // Just load starting from the 1st numerical line.
- {
- while ( fin.good() ) { // Break out of this loop if we find a number
- getline( fin, line );
- line = moose::trim(line);
- if ( isdigit( line[0] ) )
- break;;
- if ( line[0] == '-' && line.length() > 1 && isdigit( line[1] ) )
- break;
- }
- } else { // Find plotname and then begin loading.
- while ( fin.good() ) {
- getline( fin, line );
- line = moose::trim(line);
- if ( isNamedPlot ( line, plotname ) ) {
- if ( !getline ( fin, line ) )
- return 0;
- break;
- }
- }
- }
-
- v.resize( 0 );
- do {
- if ( line.length() == 0 || line == "/newplot" || line == "/plotname" )
- break;
- v.push_back( getYcolumn( line ) );
- getline( fin, line );
- line = moose::trim(line);
- } while ( fin.good() );
-
- return ( v.size() > 0 );
+ ifstream fin( fname.c_str() );
+ if ( !fin.good() )
+ {
+ cout << "TableBase::innerLoadXplot: Failed to open file " << fname <<endl;
+ return 0;
+ }
+
+ string line;
+ // Here we advance to the first numerical line.
+ if ( plotname == "" ) // Just load starting from the 1st numerical line.
+ {
+ while ( fin.good() ) // Break out of this loop if we find a number
+ {
+ getline( fin, line );
+ line = moose::trim(line);
+ if ( isdigit( line[0] ) )
+ break;;
+ if ( line[0] == '-' && line.length() > 1 && isdigit( line[1] ) )
+ break;
+ }
+ }
+ else // Find plotname and then begin loading.
+ {
+ while ( fin.good() )
+ {
+ getline( fin, line );
+ line = moose::trim(line);
+ if ( isNamedPlot ( line, plotname ) )
+ {
+ if ( !getline ( fin, line ) )
+ return 0;
+ break;
+ }
+ }
+ }
+
+ v.resize( 0 );
+ do
+ {
+ if ( line.length() == 0 || line == "/newplot" || line == "/plotname" )
+ break;
+ v.push_back( getYcolumn( line ) );
+ getline( fin, line );
+ line = moose::trim(line);
+ }
+ while ( fin.good() );
+
+ return ( v.size() > 0 );
}
void TableBase::loadXplot( string fname, string plotname )
{
- if ( !innerLoadXplot( fname, plotname, vec_ ) ) {
- cout << "TableBase::loadXplot: unable to load data from file " << fname <<endl;
- return;
- }
+ if ( !innerLoadXplot( fname, plotname, vec_ ) )
+ {
+ cout << "TableBase::loadXplot: unable to load data from file " << fname <<endl;
+ return;
+ }
}
void TableBase::loadXplotRange( string fname, string plotname,
- unsigned int start, unsigned int end )
+ unsigned int start, unsigned int end )
{
- vector< double > temp;
- if ( !innerLoadXplot( fname, plotname, temp ) ) {
- cout << "TableBase::loadXplot: unable to load data from file " << fname <<endl;
- return;
- }
- if ( start > end || end > temp.size() ) {
- cout << "TableBase::loadXplotRange: Bad range (" << start <<
- ", " << end << "] for table of size " << temp.size() <<
- " from file " << fname << endl;
- return;
- }
- vec_.clear();
- vec_.insert( vec_.end(), temp.begin() + start, temp.begin() + end );
+ vector< double > temp;
+ if ( !innerLoadXplot( fname, plotname, temp ) )
+ {
+ cout << "TableBase::loadXplot: unable to load data from file " << fname <<endl;
+ return;
+ }
+ if ( start > end || end > temp.size() )
+ {
+ cout << "TableBase::loadXplotRange: Bad range (" << start <<
+ ", " << end << "] for table of size " << temp.size() <<
+ " from file " << fname << endl;
+ return;
+ }
+ vec_.clear();
+ vec_.insert( vec_.end(), temp.begin() + start, temp.begin() + end );
}
void TableBase::loadCSV(
- string fname, int startLine, int colNum, char separator )
+ string fname, int startLine, int colNum, char separator )
{
cout << "TODO: Not implemented yet" << endl;
}
double getRMSDiff( const vector< double >& v1, const vector< double >& v2 )
{
- unsigned int size = ( v1.size() < v2.size() ) ? v1.size() : v2.size();
- if ( size == 0 )
- return -1;
-
- double sumsq = 0;
- for ( unsigned int i = 0; i < size; ++i ) {
- double temp = v1[i] - v2[i];
- sumsq += temp * temp;
- }
- return sqrt( sumsq / size );
+ unsigned int size = ( v1.size() < v2.size() ) ? v1.size() : v2.size();
+ if ( size == 0 )
+ return -1;
+
+ double sumsq = 0;
+ for ( unsigned int i = 0; i < size; ++i )
+ {
+ double temp = v1[i] - v2[i];
+ sumsq += temp * temp;
+ }
+ return sqrt( sumsq / size );
}
double getRMS( const vector< double >& v )
{
- double sumsq = 0;
- unsigned int size = v.size();
- if ( size == 0 )
- return -1;
- for ( vector< double >::const_iterator i = v.begin(); i != v.end(); ++i)
- sumsq += *i * *i;
-
- return sqrt( sumsq / size );
+ double sumsq = 0;
+ unsigned int size = v.size();
+ if ( size == 0 )
+ return -1;
+ for ( vector< double >::const_iterator i = v.begin(); i != v.end(); ++i)
+ sumsq += *i * *i;
+
+ return sqrt( sumsq / size );
}
double getRMSRatio( const vector< double >& v1, const vector< double >& v2 )
{
- double r1 = getRMS( v1 );
- double r2 = getRMS( v2 );
- if ( v1.size() == 0 || v2.size() == 0 )
- return -1;
- if ( r1 + r2 > 1e-20 )
- return getRMSDiff( v1, v2 ) / (r1 + r2);
- return -1;
+ double r1 = getRMS( v1 );
+ double r2 = getRMS( v2 );
+ if ( v1.size() == 0 || v2.size() == 0 )
+ return -1;
+ if ( r1 + r2 > 1e-20 )
+ return getRMSDiff( v1, v2 ) / (r1 + r2);
+ return -1;
}
string headop( const string& op )
{
- const unsigned int len = 5;
- char temp[len];
- unsigned int i = 0;
- for ( i = 0; i < op.length() && i < len-1 ; ++i )
- temp[i] = tolower( op[i] );
- temp[i] = '\0';
- return string( temp );
+ const unsigned int len = 5;
+ char temp[len];
+ unsigned int i = 0;
+ for ( i = 0; i < op.length() && i < len-1 ; ++i )
+ temp[i] = tolower( op[i] );
+ temp[i] = '\0';
+ return string( temp );
}
void TableBase::compareXplot( string fname, string plotname, string op )
{
- vector< double > temp;
- if ( !innerLoadXplot( fname, plotname, temp ) ) {
- cout << "TableBase::compareXplot: unable to load data from file " << fname <<endl;
- }
-
- string hop = headop( op );
-
- if ( hop == "rmsd" ) { // RMSDifference
- output_ = getRMSDiff( vec_, temp );
- }
-
- if ( hop == "rmsr" ) { // RMS ratio
- output_ = getRMSRatio( vec_, temp );
- }
-
- if ( hop == "dotp" )
- cout << "TableBase::compareXplot: DotProduct not yet done\n";
+ vector< double > temp;
+ if ( !innerLoadXplot( fname, plotname, temp ) )
+ {
+ cout << "TableBase::compareXplot: unable to load data from file " << fname <<endl;
+ }
+
+ string hop = headop( op );
+
+ if ( hop == "rmsd" ) // RMSDifference
+ {
+ output_ = getRMSDiff( vec_, temp );
+ }
+
+ if ( hop == "rmsr" ) // RMS ratio
+ {
+ output_ = getRMSRatio( vec_, temp );
+ }
+
+ if ( hop == "dotp" )
+ cout << "TableBase::compareXplot: DotProduct not yet done\n";
}
void TableBase::compareVec( vector< double > temp, string op )
{
- // Note that this line below is illegal: it causes a race condition
- // vector< double > temp = Field< vector< double > >::get( other, "vec" );
+ // Note that this line below is illegal: it causes a race condition
+ // vector< double > temp = Field< vector< double > >::get( other, "vec" );
- string hop = headop( op );
+ string hop = headop( op );
- if ( hop == "rmsd" ) { // RMSDifference
- output_ = getRMSDiff( vec_, temp );
- }
+ if ( hop == "rmsd" ) // RMSDifference
+ {
+ output_ = getRMSDiff( vec_, temp );
+ }
- if ( hop == "rmsr" ) { // RMS ratio
- output_ = getRMSRatio( vec_, temp );
- }
+ if ( hop == "rmsr" ) // RMS ratio
+ {
+ output_ = getRMSRatio( vec_, temp );
+ }
- if ( hop == "dotp" )
- cout << "TableBase::compareVec: DotProduct not yet done\n";
+ if ( hop == "dotp" )
+ cout << "TableBase::compareVec: DotProduct not yet done\n";
}
void TableBase::clearVec()
{
- vec_.resize( 0 );
+ vec_.resize(0);
}
//////////////////////////////////////////////////////////////
@@ -422,47 +450,47 @@ void TableBase::clearVec()
double TableBase::getOutputValue() const
{
- return output_;
+ return output_;
}
void TableBase::setOutputValue( double v )
{
- output_ = v;
+ output_ = v;
}
double TableBase::getY( unsigned int index ) const
{
- if ( index < vec_.size() )
- return ( vec_[index] );
- return 0;
+ if ( index < vec_.size() )
+ return ( vec_[index] );
+ return 0;
}
double TableBase::interpolate( double xmin, double xmax, double input )
- const
+const
{
- if ( vec_.size() == 0 )
- return 0;
- if ( vec_.size() == 1 || input < xmin || xmin >= xmax )
- return vec_[0];
- if ( input > xmax )
- return ( vec_.back() );
+ if ( vec_.size() == 0 )
+ return 0;
+ if ( vec_.size() == 1 || input < xmin || xmin >= xmax )
+ return vec_[0];
+ if ( input > xmax )
+ return ( vec_.back() );
- unsigned int xdivs = vec_.size() - 1;
+ unsigned int xdivs = vec_.size() - 1;
- double fraction = ( input - xmin ) / ( xmax - xmin );
- if ( fraction < 0 )
- return vec_[0];
+ double fraction = ( input - xmin ) / ( xmax - xmin );
+ if ( fraction < 0 )
+ return vec_[0];
- unsigned int j = xdivs * fraction;
- if ( j >= ( vec_.size() - 1 ) )
- return vec_.back();
+ unsigned int j = xdivs * fraction;
+ if ( j >= ( vec_.size() - 1 ) )
+ return vec_.back();
- double dx = (xmax - xmin ) / xdivs;
- double lowerBound = xmin + j * dx;
- double subFraction = ( input - lowerBound ) / dx;
+ double dx = (xmax - xmin ) / xdivs;
+ double lowerBound = xmin + j * dx;
+ double subFraction = ( input - lowerBound ) / dx;
- double y = vec_[j] + ( vec_[j + 1] - vec_[j] ) * subFraction;
- return y;
+ double y = vec_[j] + ( vec_[j + 1] - vec_[j] ) * subFraction;
+ return y;
}
//////////////////////////////////////////////////////////////
@@ -471,27 +499,27 @@ double TableBase::interpolate( double xmin, double xmax, double input )
void TableBase::setVecSize( unsigned int num )
{
- vec_.resize( num );
+ vec_.resize( num );
}
unsigned int TableBase::getVecSize() const
{
- return vec_.size();
+ return vec_.size();
}
vector< double > TableBase::getVec() const
{
- return vec_;
+ return vec_;
}
void TableBase::setVec( vector< double > val )
{
- vec_ = val;
+ vec_ = val;
}
vector< double >& TableBase::vec()
{
- return vec_;
+ return vec_;
}
// Fetch the const copy of table. Used in Streamer class.
@@ -502,18 +530,18 @@ const vector< double >& TableBase::data( )
string TableBase::getPlotDump() const
{
- static string ret = "plot.Dump";
- return ret;
+ static string ret = "plot.Dump";
+ return ret;
}
void TableBase::setPlotDump( string v )
{
-
- std::size_t pos = v.rfind(" ");
- string fname = v.substr( 0, pos );
- string plotname = "plot";
- if ( pos != string::npos )
- plotname = v.substr( pos );
- // cout << "setPlotDump( " << fname << ", " << plotname << " ), " << v << "\n";
- xplot( fname, plotname );
+
+ std::size_t pos = v.rfind(" ");
+ string fname = v.substr( 0, pos );
+ string plotname = "plot";
+ if ( pos != string::npos )
+ plotname = v.substr( pos );
+ // cout << "setPlotDump( " << fname << ", " << plotname << " ), " << v << "\n";
+ xplot( fname, plotname );
}
diff --git a/moose-core/builtins/TableBase.h b/moose-core/builtins/TableBase.h
index ada46bec7d4a544fd8dde22fbf84891dd101fb2e..d04389711a9c1445436643069541e08ac2eacf76 100644
--- a/moose-core/builtins/TableBase.h
+++ b/moose-core/builtins/TableBase.h
@@ -32,8 +32,8 @@ public:
double getOutputValue() const;
void setOutputValue( double val );
- string getPlotDump() const;
- void setPlotDump( string v );
+ string getPlotDump() const;
+ void setPlotDump( string v );
double getY( unsigned int index ) const;
diff --git a/moose-core/hsolve/HSolveActive.cpp b/moose-core/hsolve/HSolveActive.cpp
index 662c4cc80f5b9eac11258b2c8257568f0928810d..ecb48c4baac39b1c5322a74080d0af635cbbefd6 100644
--- a/moose-core/hsolve/HSolveActive.cpp
+++ b/moose-core/hsolve/HSolveActive.cpp
@@ -63,6 +63,7 @@ void HSolveActive::step( ProcPtr info )
sendValues( info );
sendSpikes( info );
+ prevExtCurr_ = externalCurrent_;
externalCurrent_.assign( externalCurrent_.size(), 0.0 );
}
diff --git a/moose-core/hsolve/HSolveActive.h b/moose-core/hsolve/HSolveActive.h
index affc85256102626d53b4a5da1bfb7baad578c8df..ad2fd46dce1a2395c8913e0a27c2a0825af2565f 100644
--- a/moose-core/hsolve/HSolveActive.h
+++ b/moose-core/hsolve/HSolveActive.h
@@ -119,6 +119,7 @@ protected:
vector< double > externalCurrent_; ///< External currents from
///< channels that HSolve
///< cannot internalize.
+ vector< double > prevExtCurr_; ///< Last tick's externalCurrent
vector< double > externalCalcium_; /// calcium from difshells
vector< Id > caConcId_; ///< Used for localIndex-ing.
vector< Id > channelId_; ///< Used for localIndex-ing.
diff --git a/moose-core/hsolve/HSolveActiveSetup.cpp b/moose-core/hsolve/HSolveActiveSetup.cpp
index 55edc3be10e53dc538cf91cb4951365d00c7b62c..5ba896116596239e664cf50cafa25816dc64884f 100644
--- a/moose-core/hsolve/HSolveActiveSetup.cpp
+++ b/moose-core/hsolve/HSolveActiveSetup.cpp
@@ -584,6 +584,7 @@ void HSolveActive::readExternalChannels()
//~ externalChannelId_.resize( compartmentId_.size() );
externalCurrent_.resize( 2 * compartmentId_.size(), 0.0 );
+ prevExtCurr_.resize( externalCurrent_.size(), 0.0 );
//~ for ( unsigned int ic = 0; ic < compartmentId_.size(); ++ic )
//~ HSolveUtils::targets(
diff --git a/moose-core/hsolve/HSolveInterface.cpp b/moose-core/hsolve/HSolveInterface.cpp
index 548646dd96a1af2b32c07d4390b39cbe795e887c..455c8cb7b9157d06f87821deda1a53f70c5020b6 100644
--- a/moose-core/hsolve/HSolveInterface.cpp
+++ b/moose-core/hsolve/HSolveInterface.cpp
@@ -170,6 +170,8 @@ double HSolve::getIm( Id id ) const
for ( ; icurrent < currentBoundary_[ index ]; ++icurrent )
Im += ( icurrent->Ek - V_[ index ] ) * icurrent->Gk;
+ assert( 2 * index + 1 < externalCurrent_.size() );
+ Im += prevExtCurr_[2*index+1] - prevExtCurr_[2*index]*V_[index];
return Im;
}
diff --git a/moose-core/ksolve/testKsolve.cpp b/moose-core/ksolve/testKsolve.cpp
index 64ae8db71ebe0f9846643d25352757901dcaacc4..12c0eb88aa3fff185a58295b2aa46f94d0c8d7bb 100644
--- a/moose-core/ksolve/testKsolve.cpp
+++ b/moose-core/ksolve/testKsolve.cpp
@@ -34,309 +34,313 @@
*/
Id makeReacTest()
{
- double simDt = 0.1;
- double plotDt = 0.1;
- Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
-
- Id pools[10];
- unsigned int i = 0;
- // Make the objects.
- Id kin = s->doCreate( "CubeMesh", Id(), "kinetics", 1 );
- Id tab = s->doCreate( "StimulusTable", kin, "tab", 1 );
- Id T = pools[i++] = s->doCreate( "BufPool", kin, "T", 1 );
- Id A = pools[i++] = s->doCreate( "Pool", kin, "A", 1 );
- Id B = pools[i++] = s->doCreate( "Pool", kin, "B", 1 );
- Id C = pools[i++] = s->doCreate( "Pool", kin, "C", 1 );
- Id D = pools[i++] = s->doCreate( "Pool", kin, "D", 1 );
- Id E = pools[i++] = s->doCreate( "Pool", kin, "E", 1 );
- Id tot1 = pools[i++] = s->doCreate( "BufPool", kin, "tot1", 1 );
- Id sum = s->doCreate( "Function", tot1, "func", 1 ); // Silly that it has to have this name.
- Id sumInput( sum.value() + 1 );
- Id e1Pool = s->doCreate( "Pool", kin, "e1Pool", 1 );
- Id e2Pool = s->doCreate( "Pool", kin, "e2Pool", 1 );
- Id e1 = s->doCreate( "Enz", e1Pool, "e1", 1 );
- Id cplx = s->doCreate( "Pool", e1, "cplx", 1 );
- Id e2 = s->doCreate( "MMenz", e2Pool, "e2", 1 );
- Id r1 = s->doCreate( "Reac", kin, "r1", 1 );
- Id r2 = s->doCreate( "Reac", kin, "r2", 1 );
- Id plots = s->doCreate( "Table2", kin, "plots", 7 );
-
- // Connect them up
- s->doAddMsg( "Single", tab, "output", T, "setN" );
-
- s->doAddMsg( "Single", r1, "sub", T, "reac" );
- s->doAddMsg( "Single", r1, "sub", A, "reac" );
- s->doAddMsg( "Single", r1, "prd", B, "reac" );
-
- Field< unsigned int >::set( sum, "numVars", 2 );
- s->doAddMsg( "Single", A, "nOut", ObjId( sumInput, 0, 0 ), "input" );
- s->doAddMsg( "Single", B, "nOut", ObjId( sumInput, 0, 1 ), "input" );
- s->doAddMsg( "Single", sum, "valueOut", tot1, "setN" );
-
- s->doAddMsg( "Single", r2, "sub", B, "reac" );
- s->doAddMsg( "Single", r2, "sub", B, "reac" );
- s->doAddMsg( "Single", r2, "prd", C, "reac" );
-
- s->doAddMsg( "Single", e1, "sub", C, "reac" );
- s->doAddMsg( "Single", e1, "enz", e1Pool, "reac" );
- s->doAddMsg( "Single", e1, "cplx", cplx, "reac" );
- s->doAddMsg( "Single", e1, "prd", D, "reac" );
-
- s->doAddMsg( "Single", e2, "sub", D, "reac" );
- s->doAddMsg( "Single", e2Pool, "nOut", e2, "enzDest" );
- s->doAddMsg( "Single", e2, "prd", E, "reac" );
-
- // Set parameters.
- Field< double >::set( A, "concInit", 2 );
- Field< double >::set( e1Pool, "concInit", 1 );
- Field< double >::set( e2Pool, "concInit", 1 );
- Field< string >::set( sum, "expr", "x0+x1" );
- Field< double >::set( r1, "Kf", 0.2 );
- Field< double >::set( r1, "Kb", 0.1 );
- Field< double >::set( r2, "Kf", 0.1 );
- Field< double >::set( r2, "Kb", 0.0 );
- Field< double >::set( e1, "Km", 5 );
- Field< double >::set( e1, "kcat", 1 );
- Field< double >::set( e1, "ratio", 4 );
- Field< double >::set( e2, "Km", 5 );
- Field< double >::set( e2, "kcat", 1 );
- vector< double > stim( 100, 0.0 );
- double vol = Field< double >::get( kin, "volume" );
- for ( unsigned int i = 0; i< 100; ++i ) {
- stim[i] = vol * NA * (1.0 + sin( i * 2.0 * PI / 100.0 ) );
- }
- Field< vector< double > >::set( tab, "vector", stim );
- Field< double >::set( tab, "stepSize", 0.0 );
- Field< double >::set( tab, "stopTime", 10.0 );
- Field< double >::set( tab, "loopTime", 10.0 );
- Field< bool >::set( tab, "doLoop", true );
-
-
- // Connect outputs
- for ( unsigned int i = 0; i < 7; ++i )
- s->doAddMsg( "Single", ObjId( plots,i),
- "requestOut", pools[i], "getConc" );
-
- // Schedule it.
- for ( unsigned int i = 11; i < 18; ++i )
- s->doSetClock( i, simDt );
- s->doSetClock( 18, plotDt );
- /*
- s->doUseClock( "/kinetics/##[ISA=Reac],/kinetics/##[ISA=EnzBase],/kinetics/##[ISA=SumFunc]",
- "process", 4 );
- s->doUseClock( "/kinetics/##[ISA=PoolBase]", "process", 5 );
- s->doUseClock( "/kinetics/##[ISA=StimulusTable]",
- "process", 4 );
- s->doUseClock( "/kinetics/##[ISA=Table]", "process", 8 );
- s->doSetClock( 4, simDt );
- s->doSetClock( 5, simDt );
- s->doSetClock( 8, plotDt );
- */
- return kin;
+ double simDt = 0.1;
+ double plotDt = 0.1;
+ Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
+
+ Id pools[10];
+ unsigned int i = 0;
+ // Make the objects.
+ Id kin = s->doCreate( "CubeMesh", Id(), "kinetics", 1 );
+ Id tab = s->doCreate( "StimulusTable", kin, "tab", 1 );
+ Id T = pools[i++] = s->doCreate( "BufPool", kin, "T", 1 );
+ Id A = pools[i++] = s->doCreate( "Pool", kin, "A", 1 );
+ Id B = pools[i++] = s->doCreate( "Pool", kin, "B", 1 );
+ Id C = pools[i++] = s->doCreate( "Pool", kin, "C", 1 );
+ Id D = pools[i++] = s->doCreate( "Pool", kin, "D", 1 );
+ Id E = pools[i++] = s->doCreate( "Pool", kin, "E", 1 );
+ Id tot1 = pools[i++] = s->doCreate( "BufPool", kin, "tot1", 1 );
+ Id sum = s->doCreate( "Function", tot1, "func", 1 ); // Silly that it has to have this name.
+ Id sumInput( sum.value() + 1 );
+ Id e1Pool = s->doCreate( "Pool", kin, "e1Pool", 1 );
+ Id e2Pool = s->doCreate( "Pool", kin, "e2Pool", 1 );
+ Id e1 = s->doCreate( "Enz", e1Pool, "e1", 1 );
+ Id cplx = s->doCreate( "Pool", e1, "cplx", 1 );
+ Id e2 = s->doCreate( "MMenz", e2Pool, "e2", 1 );
+ Id r1 = s->doCreate( "Reac", kin, "r1", 1 );
+ Id r2 = s->doCreate( "Reac", kin, "r2", 1 );
+ Id plots = s->doCreate( "Table2", kin, "plots", 7 );
+
+ // Connect them up
+ s->doAddMsg( "Single", tab, "output", T, "setN" );
+
+ s->doAddMsg( "Single", r1, "sub", T, "reac" );
+ s->doAddMsg( "Single", r1, "sub", A, "reac" );
+ s->doAddMsg( "Single", r1, "prd", B, "reac" );
+
+ Field< unsigned int >::set( sum, "numVars", 2 );
+ s->doAddMsg( "Single", A, "nOut", ObjId( sumInput, 0, 0 ), "input" );
+ s->doAddMsg( "Single", B, "nOut", ObjId( sumInput, 0, 1 ), "input" );
+ s->doAddMsg( "Single", sum, "valueOut", tot1, "setN" );
+
+ s->doAddMsg( "Single", r2, "sub", B, "reac" );
+ s->doAddMsg( "Single", r2, "sub", B, "reac" );
+ s->doAddMsg( "Single", r2, "prd", C, "reac" );
+
+ s->doAddMsg( "Single", e1, "sub", C, "reac" );
+ s->doAddMsg( "Single", e1, "enz", e1Pool, "reac" );
+ s->doAddMsg( "Single", e1, "cplx", cplx, "reac" );
+ s->doAddMsg( "Single", e1, "prd", D, "reac" );
+
+ s->doAddMsg( "Single", e2, "sub", D, "reac" );
+ s->doAddMsg( "Single", e2Pool, "nOut", e2, "enzDest" );
+ s->doAddMsg( "Single", e2, "prd", E, "reac" );
+
+ // Set parameters.
+ Field< double >::set( A, "concInit", 2 );
+ Field< double >::set( e1Pool, "concInit", 1 );
+ Field< double >::set( e2Pool, "concInit", 1 );
+ Field< string >::set( sum, "expr", "x0+x1" );
+ Field< double >::set( r1, "Kf", 0.2 );
+ Field< double >::set( r1, "Kb", 0.1 );
+ Field< double >::set( r2, "Kf", 0.1 );
+ Field< double >::set( r2, "Kb", 0.0 );
+ Field< double >::set( e1, "Km", 5 );
+ Field< double >::set( e1, "kcat", 1 );
+ Field< double >::set( e1, "ratio", 4 );
+ Field< double >::set( e2, "Km", 5 );
+ Field< double >::set( e2, "kcat", 1 );
+ vector< double > stim( 100, 0.0 );
+ double vol = Field< double >::get( kin, "volume" );
+ for ( unsigned int i = 0; i< 100; ++i )
+ {
+ stim[i] = vol * NA * (1.0 + sin( i * 2.0 * PI / 100.0 ) );
+ }
+ Field< vector< double > >::set( tab, "vector", stim );
+ Field< double >::set( tab, "stepSize", 0.0 );
+ Field< double >::set( tab, "stopTime", 10.0 );
+ Field< double >::set( tab, "loopTime", 10.0 );
+ Field< bool >::set( tab, "doLoop", true );
+
+
+ // Connect outputs
+ for ( unsigned int i = 0; i < 7; ++i )
+ s->doAddMsg( "Single", ObjId( plots,i),
+ "requestOut", pools[i], "getConc" );
+
+ // Schedule it.
+ for ( unsigned int i = 11; i < 18; ++i )
+ s->doSetClock( i, simDt );
+ s->doSetClock( 18, plotDt );
+ /*
+ s->doUseClock( "/kinetics/##[ISA=Reac],/kinetics/##[ISA=EnzBase],/kinetics/##[ISA=SumFunc]",
+ "process", 4 );
+ s->doUseClock( "/kinetics/##[ISA=PoolBase]", "process", 5 );
+ s->doUseClock( "/kinetics/##[ISA=StimulusTable]",
+ "process", 4 );
+ s->doUseClock( "/kinetics/##[ISA=Table]", "process", 8 );
+ s->doSetClock( 4, simDt );
+ s->doSetClock( 5, simDt );
+ s->doSetClock( 8, plotDt );
+ */
+ return kin;
}
void testSetupReac()
{
- Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
- Id kin = makeReacTest();
- s->doReinit();
- s->doStart( 20.0 );
- Id plots( "/kinetics/plots" );
- /*
- for ( unsigned int i = 0; i < 7; ++i ) {
- stringstream ss;
- ss << "plot." << i;
- SetGet2< string, string >::set( ObjId( plots, i ), "xplot",
- "tsr.plot", ss.str() );
- }
- */
- s->doDelete( kin );
- cout << "." << flush;
+ Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
+ Id kin = makeReacTest();
+ s->doReinit();
+ s->doStart( 20.0 );
+ Id plots( "/kinetics/plots" );
+ /*
+ for ( unsigned int i = 0; i < 7; ++i ) {
+ stringstream ss;
+ ss << "plot." << i;
+ SetGet2< string, string >::set( ObjId( plots, i ), "xplot",
+ "tsr.plot", ss.str() );
+ }
+ */
+ s->doDelete( kin );
+ cout << "." << flush;
}
void testBuildStoich()
{
- // In the updated version, we have reordered all pools and reacs by
- // Id number, modulo varPools then bufPOols.
- // Matrix looks like:
- // Reac Name R1 R2 e1a e1b e2
- // MolName
- // D -1 0 0 0 0
- // A -1 0 0 0 0
- // B +1 -2 0 0 0
- // C 0 +1 -1 0 0
- // enz1 0 0 -1 +1 0
- // e1cplx 0 0 +1 -1 0
- // E 0 0 0 +1 -1
- // F 0 0 0 0 +1
- // enz2 0 0 0 0 0
- // tot1 0 0 0 0 0
- //
- // This has been shuffled to:
- // A -1 0 0 0 0
- // B +1 -2 0 0 0
- // C 0 +1 -1 0 0
- // E 0 0 0 +1 -1
- // F 0 0 0 0 +1
- // enz1 0 0 -1 +1 0
- // enz2 0 0 0 0 0
- // e1cplx 0 0 +1 -1 0
- // D -1 0 0 0 0
- // tot1 0 0 0 0 0
- //
- // (This is the output of the print command on the sparse matrix.)
- //
- Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
- Id kin = makeReacTest();
- Id ksolve = s->doCreate( "Ksolve", kin, "ksolve", 1 );
- Id stoich = s->doCreate( "Stoich", ksolve, "stoich", 1 );
- Field< Id >::set( stoich, "compartment", kin );
- Field< Id >::set( stoich, "ksolve", ksolve );
-
- // Used to get at the stoich matrix from gdb.
+ // In the updated version, we have reordered all pools and reacs by
+ // Id number, modulo varPools then bufPOols.
+ // Matrix looks like:
+ // Reac Name R1 R2 e1a e1b e2
+ // MolName
+ // D -1 0 0 0 0
+ // A -1 0 0 0 0
+ // B +1 -2 0 0 0
+ // C 0 +1 -1 0 0
+ // enz1 0 0 -1 +1 0
+ // e1cplx 0 0 +1 -1 0
+ // E 0 0 0 +1 -1
+ // F 0 0 0 0 +1
+ // enz2 0 0 0 0 0
+ // tot1 0 0 0 0 0
+ //
+ // This has been shuffled to:
+ // A -1 0 0 0 0
+ // B +1 -2 0 0 0
+ // C 0 +1 -1 0 0
+ // E 0 0 0 +1 -1
+ // F 0 0 0 0 +1
+ // enz1 0 0 -1 +1 0
+ // enz2 0 0 0 0 0
+ // e1cplx 0 0 +1 -1 0
+ // D -1 0 0 0 0
+ // tot1 0 0 0 0 0
+ //
+ // (This is the output of the print command on the sparse matrix.)
+ //
+ Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
+ Id kin = makeReacTest();
+ Id ksolve = s->doCreate( "Ksolve", kin, "ksolve", 1 );
+ Id stoich = s->doCreate( "Stoich", ksolve, "stoich", 1 );
+ Field< Id >::set( stoich, "compartment", kin );
+ Field< Id >::set( stoich, "ksolve", ksolve );
+
+ // Used to get at the stoich matrix from gdb.
#ifndef NDEBUG
- Stoich* stoichPtr = reinterpret_cast< Stoich* >( stoich.eref().data() );
+ Stoich* stoichPtr = reinterpret_cast< Stoich* >( stoich.eref().data() );
#endif
- Field< string >::set( stoich, "path", "/kinetics/##" );
-
- unsigned int n = Field< unsigned int >::get( stoich, "numAllPools" );
- assert( n == 10 );
- unsigned int r = Field< unsigned int >::get( stoich, "numRates" );
- assert( r == 5 ); // One each for reacs and MMenz, two for Enz.
-
- vector< int > entries = Field< vector< int > >::get( stoich,
- "matrixEntry" );
- vector< unsigned int > colIndex = Field< vector< unsigned int > >::get(
- stoich, "columnIndex" );
- vector< unsigned int > rowStart = Field< vector< unsigned int > >::get(
- stoich, "rowStart" );
-
- assert( rowStart.size() == n + 1 );
- assert( entries.size() == colIndex.size() );
- assert( entries.size() == 13 );
- assert( entries[0] == -1 );
- assert( entries[1] == 1 );
- assert( entries[2] == -2 );
- assert( entries[3] == 1 );
- assert( entries[4] == -1 );
- assert( entries[5] == 1 );
- assert( entries[6] == -1 );
- assert( entries[7] == 1 );
- assert( entries[8] == -1 );
- assert( entries[9] == 1 );
- assert( entries[10] == 1 );
- assert( entries[11] == -1 );
- assert( entries[12] == -1 );
-
- s->doDelete( kin );
- cout << "." << flush;
+ Field< string >::set( stoich, "path", "/kinetics/##" );
+
+ unsigned int n = Field< unsigned int >::get( stoich, "numAllPools" );
+ assert( n == 10 );
+ unsigned int r = Field< unsigned int >::get( stoich, "numRates" );
+ assert( r == 5 ); // One each for reacs and MMenz, two for Enz.
+
+ vector< int > entries = Field< vector< int > >::get( stoich,
+ "matrixEntry" );
+ vector< unsigned int > colIndex = Field< vector< unsigned int > >::get(
+ stoich, "columnIndex" );
+ vector< unsigned int > rowStart = Field< vector< unsigned int > >::get(
+ stoich, "rowStart" );
+
+ assert( rowStart.size() == n + 1 );
+ assert( entries.size() == colIndex.size() );
+ assert( entries.size() == 13 );
+ assert( entries[0] == -1 );
+ assert( entries[1] == 1 );
+ assert( entries[2] == -2 );
+ assert( entries[3] == 1 );
+ assert( entries[4] == -1 );
+ assert( entries[5] == 1 );
+ assert( entries[6] == -1 );
+ assert( entries[7] == 1 );
+ assert( entries[8] == -1 );
+ assert( entries[9] == 1 );
+ assert( entries[10] == 1 );
+ assert( entries[11] == -1 );
+ assert( entries[12] == -1 );
+
+ s->doDelete( kin );
+ cout << "." << flush;
}
void testRunKsolve()
{
- double simDt = 0.1;
- // double plotDt = 0.1;
- Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
- Id kin = makeReacTest();
- Id ksolve = s->doCreate( "Ksolve", kin, "ksolve", 1 );
- Id stoich = s->doCreate( "Stoich", ksolve, "stoich", 1 );
- Field< Id >::set( stoich, "compartment", kin );
- Field< Id >::set( stoich, "ksolve", ksolve );
- Field< string >::set( stoich, "path", "/kinetics/##" );
- s->doUseClock( "/kinetics/ksolve", "process", 4 );
- s->doSetClock( 4, simDt );
-
- s->doReinit();
- s->doStart( 20.0 );
- Id plots( "/kinetics/plots" );
- for ( unsigned int i = 0; i < 7; ++i ) {
- stringstream ss;
- ss << "plot." << i;
- SetGet2< string, string >::set( ObjId( plots, i ), "xplot",
- "tsr2.plot", ss.str() );
- }
- s->doDelete( kin );
- cout << "." << flush;
+ double simDt = 0.1;
+ // double plotDt = 0.1;
+ Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
+ Id kin = makeReacTest();
+ Id ksolve = s->doCreate( "Ksolve", kin, "ksolve", 1 );
+ Id stoich = s->doCreate( "Stoich", ksolve, "stoich", 1 );
+ Field< Id >::set( stoich, "compartment", kin );
+ Field< Id >::set( stoich, "ksolve", ksolve );
+ Field< string >::set( stoich, "path", "/kinetics/##" );
+ s->doUseClock( "/kinetics/ksolve", "process", 4 );
+ s->doSetClock( 4, simDt );
+
+ s->doReinit();
+ s->doStart( 20.0 );
+ Id plots( "/kinetics/plots" );
+ for ( unsigned int i = 0; i < 7; ++i )
+ {
+ stringstream ss;
+ ss << "plot." << i;
+ SetGet2< string, string >::set( ObjId( plots, i ), "xplot",
+ "tsr2.plot", ss.str() );
+ }
+ s->doDelete( kin );
+ cout << "." << flush;
}
void testRunGsolve()
{
- double simDt = 0.1;
- // double plotDt = 0.1;
- Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
- Id kin = makeReacTest();
- double volume = 1e-21;
- Field< double >::set( kin, "volume", volume );
- Field< double >::set( ObjId( "/kinetics/A" ), "concInit", 2 );
- Field< double >::set( ObjId( "/kinetics/e1Pool" ), "concInit", 1 );
- Field< double >::set( ObjId( "/kinetics/e2Pool" ), "concInit", 1 );
- Id e1( "/kinetics/e1Pool/e1" );
- Field< double >::set( e1, "Km", 5 );
- Field< double >::set( e1, "kcat", 1 );
- vector< double > stim( 100, 0.0 );
- for ( unsigned int i = 0; i< 100; ++i ) {
- stim[i] = volume * NA * (1.0 + sin( i * 2.0 * PI / 100.0 ) );
- }
- Field< vector< double > >::set( ObjId( "/kinetics/tab" ), "vector", stim );
-
-
- Id gsolve = s->doCreate( "Gsolve", kin, "gsolve", 1 );
- Id stoich = s->doCreate( "Stoich", gsolve, "stoich", 1 );
- Field< Id >::set( stoich, "compartment", kin );
- Field< Id >::set( stoich, "ksolve", gsolve );
-
- Field< string >::set( stoich, "path", "/kinetics/##" );
- s->doUseClock( "/kinetics/gsolve", "process", 4 );
- s->doSetClock( 4, simDt );
-
- s->doReinit();
- s->doStart( 20.0 );
- Id plots( "/kinetics/plots" );
- for ( unsigned int i = 0; i < 7; ++i ) {
- stringstream ss;
- ss << "plot." << i;
- SetGet2< string, string >::set( ObjId( plots, i ), "xplot",
- "tsr3.plot", ss.str() );
- }
- s->doDelete( kin );
- cout << "." << flush;
+ double simDt = 0.1;
+ // double plotDt = 0.1;
+ Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
+ Id kin = makeReacTest();
+ double volume = 1e-21;
+ Field< double >::set( kin, "volume", volume );
+ Field< double >::set( ObjId( "/kinetics/A" ), "concInit", 2 );
+ Field< double >::set( ObjId( "/kinetics/e1Pool" ), "concInit", 1 );
+ Field< double >::set( ObjId( "/kinetics/e2Pool" ), "concInit", 1 );
+ Id e1( "/kinetics/e1Pool/e1" );
+ Field< double >::set( e1, "Km", 5 );
+ Field< double >::set( e1, "kcat", 1 );
+ vector< double > stim( 100, 0.0 );
+ for ( unsigned int i = 0; i< 100; ++i )
+ {
+ stim[i] = volume * NA * (1.0 + sin( i * 2.0 * PI / 100.0 ) );
+ }
+ Field< vector< double > >::set( ObjId( "/kinetics/tab" ), "vector", stim );
+
+
+ Id gsolve = s->doCreate( "Gsolve", kin, "gsolve", 1 );
+ Id stoich = s->doCreate( "Stoich", gsolve, "stoich", 1 );
+ Field< Id >::set( stoich, "compartment", kin );
+ Field< Id >::set( stoich, "ksolve", gsolve );
+
+ Field< string >::set( stoich, "path", "/kinetics/##" );
+ s->doUseClock( "/kinetics/gsolve", "process", 4 );
+ s->doSetClock( 4, simDt );
+
+ s->doReinit();
+ s->doStart( 20.0 );
+ Id plots( "/kinetics/plots" );
+ for ( unsigned int i = 0; i < 7; ++i )
+ {
+ stringstream ss;
+ ss << "plot." << i;
+ SetGet2< string, string >::set( ObjId( plots, i ), "xplot",
+ "tsr3.plot", ss.str() );
+ }
+ s->doDelete( kin );
+ cout << "." << flush;
}
void testFuncTerm()
{
- FuncTerm ft;
- ft.setExpr( "x0 + x1 * t" );
- double args[] = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 };
-
- // First check that it doesn't die even if we forget to set up anything.
- double ans = ft( args, 2.0 );
-
- vector< unsigned int > mol( 2, 0 );
- mol[0] = 2;
- mol[1] = 0;
- ft.setReactantIndex( mol );
-
- ans = ft( args, 10.0 );
- assert( doubleEq( ans, 13.0 ) );
- mol[0] = 0;
- mol[1] = 9;
- ft.setReactantIndex( mol );
- ans = ft( args, 2.0 );
- assert( doubleEq( ans, 21.0 ) );
- cout << "." << flush;
+ FuncTerm ft;
+ ft.setExpr( "x0 + x1 * t" );
+ double args[] = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 };
+
+ // First check that it doesn't die even if we forget to set up anything.
+ double ans = ft( args, 2.0 );
+
+ vector< unsigned int > mol( 2, 0 );
+ mol[0] = 2;
+ mol[1] = 0;
+ ft.setReactantIndex( mol );
+
+ ans = ft( args, 10.0 );
+ assert( doubleEq( ans, 13.0 ) );
+ mol[0] = 0;
+ mol[1] = 9;
+ ft.setReactantIndex( mol );
+ ans = ft( args, 2.0 );
+ assert( doubleEq( ans, 21.0 ) );
+ cout << "." << flush;
}
void testKsolve()
{
- testSetupReac();
- testBuildStoich();
- testRunKsolve();
- testRunGsolve();
- testFuncTerm();
+ testSetupReac();
+ testBuildStoich();
+ testRunKsolve();
+ testRunGsolve();
+ testFuncTerm();
}
void testKsolveProcess()
{
-;
+ ;
}
diff --git a/moose-core/pymoose/moosemodule.cpp b/moose-core/pymoose/moosemodule.cpp
index 5e811d0283737874a826f7698da7f5129d3aa4ab..0a71f46667693213040b1a899ecde7db60b771ea 100644
--- a/moose-core/pymoose/moosemodule.cpp
+++ b/moose-core/pymoose/moosemodule.cpp
@@ -17,9 +17,10 @@
#include <map>
#include <ctime>
#include <csignal>
+#include <chrono>
+#include <thread>
#include <exception>
-
#if USE_BOOST_ODE
#include <boost/format.hpp>
#endif
@@ -88,6 +89,8 @@ extern void speedTestMultiNodeIntFireNetwork(
extern void mooseBenchmarks( unsigned int option );
+// global variable.
+bool tcpSocketStreamerEnabled_ = false;
/*-----------------------------------------------------------------------------
* Random number generator for this module.
@@ -107,6 +110,31 @@ double pymoose_mtrand_( void )
return moose::mtrand( );
}
+bool setupSocketStreamer(const string addr )
+{
+ LOG(moose::debug, "Setting streamer with addr " << addr );
+
+ // Find all tables.
+ vector< ObjId > tables;
+ wildcardFind( "/##[TYPE=Table2]", tables );
+ wildcardFind( "/##[TYPE=Table]", tables, false );
+
+ if( tables.size() < 1 )
+ {
+ LOG( moose::warning, "No table found. MOOSE will not create a streamer." );
+ return false;
+ }
+
+ // Craete a SocketStreamer and add all tables.
+ Id stBase = SHELLPTR->doCreate("Neutral", Id(), "socket", 1);
+ Id st = SHELLPTR->doCreate("SocketStreamer", stBase, "streamer", 1);
+ Field<string>::set(st, "address", addr);
+
+ for( auto &t : tables )
+ SetGet1<Id>::set(st, "addTable", t.id );
+ return true;
+}
+
/**
Utility function to get all the individual elements when ALLDATA is dataIndex.
*/
@@ -1721,10 +1749,8 @@ PyObject * moose_start(PyObject * dummy, PyObject * args )
sigemptyset(&sigHandler.sa_mask);
sigHandler.sa_flags = 0;
sigaction(SIGINT, &sigHandler, NULL);
-
SHELLPTR->doStart( runtime, notify );
Py_RETURN_NONE;
-
}
PyDoc_STRVAR(moose_reinit_documentation,
@@ -1742,9 +1768,20 @@ PyDoc_STRVAR(moose_reinit_documentation,
"\n");
PyObject * moose_reinit(PyObject * dummy, PyObject * args)
{
+ // If environment variable MOOSE_TCP_STREAMER_ADDRESS is set then setup the
+ // streamer.
+ string envSocketServer = moose::getEnv( "MOOSE_STREAMER_ADDRESS" );
+ if(! envSocketServer.empty())
+ {
+ LOG( moose::debug, "Environment variable set of socket" << envSocketServer );
+ if( envSocketServer.size() > 0 )
+ setupSocketStreamer(envSocketServer);
+ }
+
SHELLPTR->doReinit();
Py_RETURN_NONE;
}
+
PyObject * moose_stop(PyObject * dummy, PyObject * args)
{
SHELLPTR->doStop();
@@ -1765,10 +1802,12 @@ PyObject * moose_exists(PyObject * dummy, PyObject * args)
return Py_BuildValue("i", Id(path) != Id() || string(path) == "/" || string(path) == "/root");
}
-PyDoc_STRVAR(moose_loadModel_documentation,
- "loadModel(filename, modelpath, solverclass) -> vec\n"
+PyDoc_STRVAR(moose_loadModelInternal_documentation,
+ "loadModelInternal(filename, modelpath, solverclass) -> vec\n"
"\n"
"Load model from a file to a specified path.\n"
+ "Note: This function should not be used by users. It is meants for developers. \n"
+ "Please see `moose.loadModel` function.\n"
"\n"
"Parameters\n"
"----------\n"
@@ -1785,11 +1824,11 @@ PyDoc_STRVAR(moose_loadModel_documentation,
" loaded model container vec.\n"
);
-PyObject * moose_loadModel(PyObject * dummy, PyObject * args)
+PyObject * moose_loadModelInternal(PyObject * dummy, PyObject * args)
{
char * fname = NULL, * modelpath = NULL, * solverclass = NULL;
- if(!PyArg_ParseTuple(args, "ss|s:moose_loadModel", &fname, &modelpath, &solverclass))
+ if(!PyArg_ParseTuple(args, "ss|s:moose_loadModelInternal", &fname, &modelpath, &solverclass))
{
cout << "here in moose load";
return NULL;
@@ -1812,7 +1851,8 @@ PyObject * moose_loadModel(PyObject * dummy, PyObject * args)
PyObject * ret = reinterpret_cast<PyObject*>(model);
return ret;
}
-/*
+
+#if 0
PyDoc_STRVAR(moose_saveModel_documentation,
"saveModel(source, filename) -> None\n"
"\n"
@@ -1869,7 +1909,8 @@ PyObject * moose_saveModel(PyObject * dummy, PyObject * args)
SHELLPTR->doSaveModel(model, filename);
Py_RETURN_NONE;
}
-*/
+#endif
+
PyObject * moose_setCwe(PyObject * dummy, PyObject * args)
{
PyObject * element = NULL;
@@ -3013,7 +3054,7 @@ static PyMethodDef MooseMethods[] =
{"stop", (PyCFunction)moose_stop, METH_VARARGS, "Stop simulation"},
{"isRunning", (PyCFunction)moose_isRunning, METH_VARARGS, "True if the simulation is currently running."},
{"exists", (PyCFunction)moose_exists, METH_VARARGS, "True if there is an object with specified path."},
- {"loadModel", (PyCFunction)moose_loadModel, METH_VARARGS, moose_loadModel_documentation},
+ {"loadModelInternal", (PyCFunction)moose_loadModelInternal, METH_VARARGS, moose_loadModelInternal_documentation},
//{"saveModel", (PyCFunction)moose_saveModel, METH_VARARGS, moose_saveModel_documentation},
{"connect", (PyCFunction)moose_connect, METH_VARARGS, moose_connect_documentation},
{"getCwe", (PyCFunction)moose_getCwe, METH_VARARGS, "Get the current working element. 'pwe' is an alias of this function."},
@@ -3232,33 +3273,3 @@ PyMODINIT_FUNC MODINIT(_moose)
return moose_module;
#endif
}
-
-
-//////////////////////////////////////////////
-// Main function
-//////////////////////////////////////////////
-
-// int main(int argc, char* argv[])
-// {
-// #ifdef PY3K
-// size_t len = strlen(argv[0]);
-// wchar_t * warg = (wchar_t*)calloc(sizeof(wchar_t), len);
-// mbstowcs(warg, argv[0], len);
-// #else
-// char * warg = argv[0];
-// #endif
-// for (int ii = 0; ii < argc; ++ii){
-// cout << "ARGV: " << argv[ii];
-// }
-// cout << endl;
-// Py_SetProgramName(warg);
-// Py_Initialize();
-// MODINIT(_moose);
-// #ifdef PY3K
-// free(warg);
-// #endif
-// return 0;
-// }
-
-//
-// moosemodule.cpp ends here
diff --git a/moose-core/pymoose/moosemodule.h b/moose-core/pymoose/moosemodule.h
index 7ef0e79375c65c8fddf49c9e4fdaec1c4807ebc1..470b17f100a17c86c51ae9ec0e5fbd4e80ea54bf 100644
--- a/moose-core/pymoose/moosemodule.h
+++ b/moose-core/pymoose/moosemodule.h
@@ -234,7 +234,7 @@ PyObject * moose_reinit(PyObject * dummy, PyObject * args);
PyObject * moose_stop(PyObject * dummy, PyObject * args);
PyObject * moose_isRunning(PyObject * dummy, PyObject * args);
PyObject * moose_exists(PyObject * dummy, PyObject * args);
-PyObject * moose_loadModel(PyObject * dummy, PyObject * args);
+PyObject * moose_loadModelInternal(PyObject * dummy, PyObject * args);
//PyObject * moose_saveModel(PyObject * dummy, PyObject * args);
PyObject * moose_setCwe(PyObject * dummy, PyObject * args);
PyObject * moose_getCwe(PyObject * dummy, PyObject * args);
diff --git a/moose-core/python/moose/SBML/readSBML.py b/moose-core/python/moose/SBML/readSBML.py
index f8e74f7e13bdd9194b60dadc4f1f17a336fdd153..356d2400314d2b4623594f8057943bdfc93031ef 100644
--- a/moose-core/python/moose/SBML/readSBML.py
+++ b/moose-core/python/moose/SBML/readSBML.py
@@ -13,10 +13,14 @@
** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
Created : Thu May 13 10:19:00 2016(+0530)
Version
-Last-Updated: Fri Oct 26 11:21:00 2018(+0530)
+Last-Updated: Tue Dec 3 17:30:00 2018(+0530)
By:HarshaRani
**********************************************************************/
2018
+Dec 3: - reading motor and diffconstant from pool
+Nov 30: - groups and subgroups are read from xml to moose
+Nov 19: - reading and creating CylMesh and EndoMesh if specified in the Annotation field in compartment
+ definition, also checking if EndoMesh missing/wrong surround compartment
Oct 26: - validator can be switchedoff by passing validate="off" while readSBML files
May 18: - cleanedup and connected cplx pool to correct parent enzyme
Jan 6: - only if valid model exists, then printing the no of compartment,pool,reaction etc
@@ -78,7 +82,7 @@ try:
except ImportError:
pass
-def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
+def mooseReadSBML(filepath, loadpath, solver="ee",validate="True"):
"""Load SBML model
"""
global foundLibSBML_
@@ -101,7 +105,7 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
filep = open(filepath, "r")
document = libsbml.readSBML(filepath)
tobecontinue = False
- if validate == "on":
+ if validate == "True":
tobecontinue = validateModel(document)
else:
tobecontinue = True
@@ -142,7 +146,8 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
globparameterIdValue = {}
mapParameter(model, globparameterIdValue)
- errorFlag = createCompartment(
+ msgCmpt = ""
+ errorFlag,msgCmpt = createCompartment(
basePath, model, comptSbmlidMooseIdMap)
groupInfo = checkGroup(basePath,model)
@@ -159,7 +164,7 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
model, specInfoMap, modelAnnotaInfo, globparameterIdValue,funcDef,groupInfo)
if len(moose.wildcardFind(moose.element(loadpath).path+"/##[ISA=ReacBase],/##[ISA=EnzBase]")) == 0:
errorFlag = False
- noRE = ("Atleast one reaction should be present ")
+ noRE = ("Atleast one reaction should be present to display in the widget ")
getModelAnnotation(
model, baseId, basePath)
if not errorFlag:
@@ -197,9 +202,9 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
moose.delete(basePath)
loadpath = moose.Shell('/')
#return basePath, ""
- loaderror = msgRule+msgReac+noRE
+ loaderror = msgCmpt+str(msgRule)+msgReac+noRE
if loaderror != "":
- loaderror = loaderror +" to display in the widget"
+ loaderror = loaderror
return moose.element(loadpath), loaderror
else:
print("Validation failed while reading the model.")
@@ -223,6 +228,7 @@ def checkFuncDef(model):
if foundbvar and foundfuncMathML:
funcDef[f.getName()] = {'bvar':bvar, "MathML": fmath.getRightChild()}
return funcDef
+
def checkGroup(basePath,model):
groupInfo = {}
modelAnnotaInfo = {}
@@ -235,26 +241,36 @@ def checkGroup(basePath,model):
groupAnnoInfo = getObjAnnotation(p, modelAnnotaInfo)
if groupAnnoInfo != {}:
if moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]):
- if not moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+p.getId()):
- moosegrp = moose.Neutral(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+p.getId())
+ if "Group" in groupAnnoInfo:
+ if moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]):
+ if moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName()):
+ moosegrp = moose.element(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName())
+ else:
+ moosegrp = moose.Neutral(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName())
+ else:
+ moose.Neutral(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"])
+ if moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName()):
+ moosegrp = moose.element(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName())
+ else:
+ moosegrp = moose.Neutral(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName())
else:
- moosegrp = moose.element(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+p.getId())
+ if not moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+p.getName()):
+ moosegrp = moose.Neutral(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+p.getName())
+ else:
+ moosegrp = moose.element(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+p.getName())
moosegrpinfo = moose.Annotator(moosegrp.path+'/info')
moosegrpinfo.color = groupAnnoInfo["bgColor"]
- else:
- print ("Compartment not found")
-
+ else:
+ print ("Compartment not found")
if p.getKind() == 2:
if p.getId() not in groupInfo:
- #groupInfo[p.getId()]
+ memlists = []
for gmemIndex in range(0,p.getNumMembers()):
mem = p.getMember(gmemIndex)
-
- if p.getId() in groupInfo:
- groupInfo[p.getId()].append(mem.getIdRef())
- else:
- groupInfo[p.getId()] =[mem.getIdRef()]
+ memlists.append(mem.getIdRef())
+ groupInfo[p.getId()] = {"mpath":moosegrp, "splist":memlists}
return groupInfo
+
def setupEnzymaticReaction(enz, groupName, enzName,
specInfoMap, modelAnnotaInfo,deletcplxMol):
enzPool = (modelAnnotaInfo[groupName]["enzyme"])
@@ -402,6 +418,36 @@ def getModelAnnotation(obj, baseId, basepath):
tablelistname.append(fullPath)
moose.connect(tab, "requestOut", plotSId, "getConc")
+def getCmptAnnotation(obj):
+ annotateMap = {}
+ if (obj.getAnnotation() is not None):
+ annoNode = obj.getAnnotation()
+ for ch in range(0, annoNode.getNumChildren()):
+ childNode = annoNode.getChild(ch)
+ if (childNode.getPrefix() == "moose" and (childNode.getName() in["CompartmentAnnotation"])):
+ 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 == "Mesh":
+ annotateMap[nodeName] = nodeValue
+ if nodeName == "numDiffCompts":
+ annotateMap[nodeName] = nodeValue
+ if nodeName == "isMembraneBound":
+ annotateMap[nodeName] = nodeValue
+ if nodeName == "totLength":
+ annotateMap[nodeName] = nodeValue
+ if nodeName == "diffLength":
+ annotateMap[nodeName] = nodeValue
+ if nodeName == "surround":
+ annotateMap[nodeName] = nodeValue
+ return annotateMap
def getObjAnnotation(obj, modelAnnotationInfo):
name = obj.getId()
@@ -436,6 +482,10 @@ def getObjAnnotation(obj, modelAnnotationInfo):
annotateMap[nodeName] = nodeValue
if nodeName == "Compartment":
annotateMap[nodeName] = nodeValue
+ if nodeName == "diffConstant":
+ annotateMap[nodeName] = nodeValue
+ if nodeName == "motorConstant":
+ annotateMap[nodeName] = nodeValue
return annotateMap
@@ -572,9 +622,13 @@ def createReaction(model, specInfoMap, modelAnnotaInfo, globparameterIdValue,fun
if (reac.isSetId()):
rId = reac.getId()
- groups = [k for k, v in groupInfo.items() if rId in v]
- if groups:
- group = groups[0]
+ #groups = [k for k, v in groupInfo.items() if rId in v]
+ for k,v in groupInfo.items():
+ if rId in v["splist"]:
+ group = v["mpath"]
+
+ # if groups:
+ # group = groups[0]
if (reac.isSetName()):
rName = reac.getName()
rName = rName.replace(" ", "_space_")
@@ -648,12 +702,12 @@ def createReaction(model, specInfoMap, modelAnnotaInfo, globparameterIdValue,fun
sp = react.getSpecies()
sp = str(idBeginWith(sp))
speCompt = specInfoMap[sp]["comptId"].path
-
if group:
- if moose.exists(speCompt+'/'+group):
- speCompt = speCompt+'/'+group
- else:
- speCompt = (moose.Neutral(speCompt+'/'+group)).path
+ speCompt = group.path
+ # if moose.exists(speCompt+'/'+group):
+ # speCompt = speCompt+'/'+group
+ # else:
+ # speCompt = (moose.Neutral(speCompt+'/'+group)).path
if moose.exists(speCompt + '/' + rName):
rName =rId
reaction_ = moose.Reac(speCompt + '/' + rName)
@@ -1092,7 +1146,6 @@ def pullnotes(sbmlId, mooseId):
objInfo = moose.element(mooseId.path + '/info')
objInfo.notes = notes
-
def createSpecies(basePath, model, comptSbmlidMooseIdMap,
specInfoMap, modelAnnotaInfo,groupInfo):
# ToDo:
@@ -1112,10 +1165,13 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
sName = None
sId = spe.getId()
-
- groups = [k for k, v in groupInfo.items() if sId in v]
- if groups:
- group = groups[0]
+ group = ""
+ #groups = [k for k, v in groupInfo.items() if sId in v]
+ for k,v in groupInfo.items():
+ if sId in v["splist"]:
+ group = v["mpath"]
+ # if groups:
+ # group = groups[0]
if spe.isSetName():
sName = spe.getName()
sName = sName.replace(" ", "_space_")
@@ -1133,10 +1189,11 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
# "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 group:
- if moose.exists(comptEl+'/'+group):
- comptEl = comptEl+'/'+group
- else:
- comptEl = (moose.Neutral(comptEl+'/'+group)).path
+ comptEl = group.path
+ # if moose.exists(comptEl+'/'+group):
+ # comptEl = comptEl+'/'+group
+ # else:
+ # comptEl = (moose.Neutral(comptEl+'/'+group)).path
if (boundaryCondition):
poolId = moose.BufPool(comptEl + '/' + sName)
else:
@@ -1159,7 +1216,10 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
poolInfo.color = v
elif k == 'Color':
poolInfo.textColor = v
-
+ elif k == 'diffConstant':
+ poolId.diffConst = float(v)
+ elif k == 'motorConstant':
+ poolId.motorConst = float(v)
specInfoMap[sId] = {
"Mpath": poolId,
"const": constant,
@@ -1220,7 +1280,6 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
return (True," ")
-
def transformUnit(unitForObject, hasonlySubUnit=False):
# print "unit
# ",UnitDefinition.printUnits(unitForObject.getDerivedUnitDefinition())
@@ -1301,10 +1360,12 @@ def transformUnit(unitForObject, hasonlySubUnit=False):
def createCompartment(basePath, model, comptSbmlidMooseIdMap):
# ToDoList : Check what should be done for the spaitialdimension is 2 or
# 1, area or length
- #print " createCompartment ",model.getNumCompartments()
+ cmptAnnotaInfo = {}
+
if not(model.getNumCompartments()):
- return False, "Model has no compartment, atleast one compartment should exist to display the widget"
+ return False, "Model has no compartment, atleast one compartment should exist to display in the widget"
else:
+ endo_surr = {}
for c in range(0, model.getNumCompartments()):
compt = model.getCompartment(c)
# print("Compartment " + str(c) + ": "+ UnitDefinition.printUnits(compt.getDerivedUnitDefinition()))
@@ -1333,18 +1394,44 @@ def createCompartment(basePath, model, comptSbmlidMooseIdMap):
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
+ return False," Currently we don't deal with spatial Dimension less than 3 and unit's area or length"
if not(name):
name = sbmlCmptId
+ cmptAnnotaInfo = {}
+ cmptAnnotaInfo = getCmptAnnotation(compt)
+ if "Mesh" in cmptAnnotaInfo.keys():
+ if cmptAnnotaInfo["Mesh"] == "CubeMesh" or cmptAnnotaInfo["Mesh"] == "NeuroMesh":
+ mooseCmptId = moose.CubeMesh(basePath.path + '/' + name)
+
+ elif cmptAnnotaInfo["Mesh"] == "CylMesh":
+ mooseCmptId = moose.CylMesh(basePath.path + '/' + name)
+ ln = (float(cmptAnnotaInfo["totLength"])/float(cmptAnnotaInfo["diffLength"]))*float(cmptAnnotaInfo["diffLength"])
+ mooseCmptId.x1 = ln
+ mooseCmptId.diffLength = float(cmptAnnotaInfo["diffLength"])
+
+ elif cmptAnnotaInfo["Mesh"] == "EndoMesh":
+ mooseCmptId = moose.EndoMesh(basePath.path + '/' + name)
+ endo_surr[sbmlCmptId] = cmptAnnotaInfo["surround"]
- mooseCmptId = moose.CubeMesh(basePath.path + '/' + name)
+ if cmptAnnotaInfo["isMembraneBound"] == 'True':
+ mooseCmptId.isMembraneBound = bool(cmptAnnotaInfo["isMembraneBound"])
+ else:
+ mooseCmptId = moose.CubeMesh(basePath.path+'/'+name)
+
mooseCmptId.volume = (msize * unitfactor)
+
comptSbmlidMooseIdMap[sbmlCmptId] = {
"MooseId": mooseCmptId, "spatialDim": dimension, "size": msize}
- return True
+
+ for key,value in endo_surr.items():
+ if value in comptSbmlidMooseIdMap:
+ endomesh = comptSbmlidMooseIdMap[key]["MooseId"]
+ endomesh.surround = comptSbmlidMooseIdMap[value]["MooseId"]
+ elif key in comptSbmlidMooseIdMap:
+ del(comptSbmlidMooseIdMap[key])
+ return False," EndoMesh's surrounding compartment missing or wrong deleting the compartment check the file"
+ return True,""
def setupMMEnzymeReaction(reac, rName, specInfoMap, reactSBMLIdMooseId,
diff --git a/moose-core/python/moose/SBML/writeSBML.py b/moose-core/python/moose/SBML/writeSBML.py
index a3d898d44c2b0c02d2f8e4f55404332f6ac9c86a..d8325ee2a978cb49af6992f48ded5daa347da607 100644
--- a/moose-core/python/moose/SBML/writeSBML.py
+++ b/moose-core/python/moose/SBML/writeSBML.py
@@ -13,11 +13,20 @@
** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
Created : Friday May 27 12:19:00 2016(+0530)
Version
-Last-Updated: Mon 30 Apr 15:10:00 2018(+0530)
+Last-Updated: Tue 3 Dec 15:15:10 2018(+0530)
By: HarshaRani
**********************************************************************/
/****************************
2018
+Dec 07: using fixXreac's restoreXreacs function to remove xfer
+Dec 03: add diff and motor constants to pool
+Nov 30: group id is changed from name to moose_id and group.name is added along with annotation for group listing
+Nov 22: searched for _xfer_ instead of xfer
+Nov 12: xfer cross compartment molecules are not written to SBML instead written the original molecule also for connecting Reaction and Enzyme
+Nov 06: All the Mesh Cyl,Cube,Neuro,Endo Mesh's can be written into SBML format with annotation field where Meshtype\
+ numDiffCompts,isMembraneBound and surround are written out.
+ For EndoMesh check made to see surround is specified
+Oct 20: EndoMesh added to SBML
Oct 16: CylMesh's comparment volume is written, but zeroth volex details are populated
Oct 13: CylMesh are written to SBML with annotation field and only zeroth element/voxel (incase of cylMesh) of moose object is written
Oct 1 : corrected the spell of CyclMesh-->CylMesh, negating the yaxis for kkit is removed
@@ -40,6 +49,7 @@ import moose
from moose.SBML.validation import validateModel
from moose.chemUtil.chemConnectUtil import *
from moose.chemUtil.graphUtils import *
+from moose.fixXreacs import restoreXreacs
foundLibSBML_ = False
try:
@@ -76,6 +86,7 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
if not moose.exists(modelpath):
return False, "Path doesn't exist"
elif moose.exists(modelpath):
+ moose.fixXreacs.restoreXreacs(modelpath)
checkCompt = moose.wildcardFind(modelpath+'/##[0][ISA=ChemCompt]')
mObj = moose.wildcardFind(moose.element(modelpath).path+'/##[0][ISA=PoolBase]'+','+
@@ -108,6 +119,7 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
neutralNotes = ""
specieslist = moose.wildcardFind(modelpath + '/##[0][ISA=PoolBase]')
+
if specieslist:
neutralPath = getGroupinfo(specieslist[0])
if moose.exists(neutralPath.path + '/info'):
@@ -124,11 +136,12 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
writeUnits(cremodel_)
modelAnno = writeSimulationAnnotation(modelpath)
+
if modelAnno:
cremodel_.setAnnotation(modelAnno)
groupInfo = {}
-
- compartexist, groupInfo = writeCompt(modelpath, cremodel_)
+ compterrors =""
+ compartexist, groupInfo,compterrors = writeCompt(modelpath, cremodel_)
if compartexist == True:
species = writeSpecies( modelpath,cremodel_,sbmlDoc,sceneitems,groupInfo)
@@ -145,20 +158,24 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
mplugin = cremodel_.getPlugin("groups")
group = mplugin.createGroup()
name = str(idBeginWith(moose.element(key).name))
- group.setId(name)
+ moosegrpId = name +"_" + str(moose.element(key).getId().value) + "_" + str(moose.element(key).getDataIndex())
+ group.setId(moosegrpId)
+ group.setName(name)
+
group.setKind("collection")
if moose.exists(key.path+'/info'):
ginfo = moose.element(key.path+'/info')
else:
ginfo = moose.Annotator(key.path+'/info')
groupCompartment = findCompartment(key)
- if ginfo.color != '':
- grpAnno = "<moose:GroupAnnotation>"
- grpAnno = grpAnno + "<moose:Compartment>" + groupCompartment.name + "</moose:Compartment>\n"
- if ginfo.color:
- grpAnno = grpAnno + "<moose:bgColor>" + ginfo.color + "</moose:bgColor>\n"
- grpAnno = grpAnno + "</moose:GroupAnnotation>"
- group.setAnnotation(grpAnno)
+ grpAnno = "<moose:GroupAnnotation>"
+ grpAnno = grpAnno + "<moose:Compartment>" + groupCompartment.name + "</moose:Compartment>\n"
+ if moose.element(key.parent).className == "Neutral":
+ grpAnno = grpAnno + "<moose:Group>" + key.parent.name + "</moose:Group>\n"
+ if ginfo.color:
+ grpAnno = grpAnno + "<moose:bgColor>" + ginfo.color + "</moose:bgColor>\n"
+ grpAnno = grpAnno + "</moose:GroupAnnotation>"
+ group.setAnnotation(grpAnno)
for values in value:
member = group.createMember()
@@ -170,13 +187,16 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
writeTofile = filepath + "/" + filename + '.xml'
writeSBMLToFile(sbmlDoc, writeTofile)
return True, consistencyMessages, writeTofile
-
+
if (not SBMLok):
#cerr << "Errors encountered " << endl
consistencyMessages = "Errors encountered"
return -1, consistencyMessages
else:
- return False, "Atleast one compartment should exist to write SBML"
+ if compterrors:
+ return False, compterrors
+ else:
+ return False,"Atleast one compartment should exist to write SBML"
def writeEnz(modelpath, cremodel_, sceneitems,groupInfo):
for enz in moose.wildcardFind(modelpath + '/##[0][ISA=EnzBase]'):
@@ -595,6 +615,15 @@ def processRateLaw(objectCount, cremodel, noofObj, type, mobjEnz):
nameList_[:] = []
for value, count in objectCount.items():
value = moose.element(value)
+ '''
+ if re.search("_xfer_",value.name):
+ modelRoot = value.path[0:value.path.index('/',1)]
+ xrefPool = value.name[:value.name.index("_xfer_")]
+ xrefCompt = value.name[value.name.index("_xfer_") + len("_xfer_"):]
+ orgCompt = moose.wildcardFind(modelRoot+'/##[FIELD(name)='+xrefCompt+']')[0]
+ orgPool = moose.wildcardFind(orgCompt.path+'/##[FIELD(name)='+xrefPool+']')[0]
+ value = orgPool
+ '''
nameIndex = value.name + "_" + \
str(value.getId().value) + "_" + str(value.getDataIndex()) + "_"
clean_name = (str(idBeginWith(convertSpecialChar(nameIndex))))
@@ -836,7 +865,7 @@ def getGroupinfo(element):
# 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", "CubeMesh", "CylMesh"]):
+ while not mooseIsInstance(element, ["Neutral", "CubeMesh", "CylMesh","EndoMesh","NeuroMesh"]):
element = element.parent
return element
@@ -848,7 +877,7 @@ def idBeginWith(name):
return changedName
def findGroup_compt(melement):
- while not (mooseIsInstance(melement, ["Neutral","CubeMesh", "CylMesh"])):
+ while not (mooseIsInstance(melement, ["Neutral","CubeMesh", "CylMesh","EndoMesh","NeuroMesh"])):
melement = melement.parent
return melement
@@ -878,82 +907,82 @@ def convertSpecialChar(str1):
def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems,speGroup):
# getting all the species
for spe in moose.wildcardFind(modelpath + '/##[0][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.setName(str(idBeginWith(convertSpecialCharshot(spe.name))))
- # s1.setInitialAmount(spe.nInit)
- s1.setInitialConcentration(spe.concInit)
- 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)
+ #Eliminating xfer molecules writting
+ if not re.search("_xfer_",spe.name):
+
+ sName = convertSpecialChar(spe.name)
+ comptVec = findCompartment(spe)
+ speciannoexist = False
+
+ if not isinstance(moose.element(comptVec), moose.ChemCompt):
+ return -2
else:
- # if not bufpool then Pool, then
- s1.setBoundaryCondition(False)
- s1.setConstant(False)
- s1.setUnits("substance")
- s1.setHasOnlySubstanceUnits(False)
- if moose.exists(spe.path + '/info'):
- Anno = moose.Annotator(spe.path + '/info')
- if Anno.notes != "":
- cleanNotesS = convertNotesSpecialChar(Anno.notes)
- notesStringS = "<body xmlns=\"http://www.w3.org/1999/xhtml\">\n \t \t" + \
- cleanNotesS + "\n\t </body>"
- s1.setNotes(notesStringS)
-
-
- element = moose.element(spe)
- ele = getGroupinfo(element)
- if element.className == "Neutral" or Anno.color or Anno.textColor or sceneitems or Anno.x or Anno.y:
- speciannoexist = True
- if speciannoexist:
+ 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.setName(str(idBeginWith(convertSpecialCharshot(spe.name))))
+ # s1.setInitialAmount(spe.nInit)
+ s1.setInitialConcentration(spe.concInit)
+ 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(False)
+ if moose.exists(spe.path + '/info'):
+ Anno = moose.Annotator(spe.path + '/info')
+ if Anno.notes != "":
+ cleanNotesS = convertNotesSpecialChar(Anno.notes)
+ notesStringS = "<body xmlns=\"http://www.w3.org/1999/xhtml\">\n \t \t" + \
+ cleanNotesS + "\n\t </body>"
+ s1.setNotes(notesStringS)
+
+
+ element = moose.element(spe)
+ ele = getGroupinfo(element)
+
speciAnno = "<moose:ModelAnnotation>\n"
if ele.className == "Neutral":
#speciAnno = speciAnno + "<moose:Group>" + ele.name + "</moose:Group>\n"
@@ -982,6 +1011,8 @@ def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems,speGroup):
if Anno.textColor:
speciAnno = speciAnno + "<moose:textColor>" + \
Anno.textColor + "</moose:textColor>\n"
+ speciAnno = speciAnno + "<moose:diffConstant>" + str(spe.diffConst) + "</moose:diffConstant>\n"
+ speciAnno = speciAnno + "<moose:motorConstant>" + str(spe.motorConst)+ "</moose:motorConstant>\n"
speciAnno = speciAnno + "</moose:ModelAnnotation>"
s1.setAnnotation(speciAnno)
return True
@@ -991,49 +1022,85 @@ def writeCompt(modelpath, cremodel_):
# getting all the compartments
compts = moose.wildcardFind(modelpath + '/##[0][ISA=ChemCompt]')
groupInfo = {}
+ comptID_sbml = {}
for compt in compts:
comptAnno = ""
comptName = convertSpecialChar(compt.name)
# converting m3 to litre
- if isinstance(compt,moose.CylMesh):
+ createCompt = True
+ size = compt.volume * pow(10, 3)
+ ndim = compt.numDimensions
+ csetId = (str(idBeginWith(comptName +
+ "_" +
+ str(compt.getId().value) +
+ "_" +
+ str(compt.getDataIndex()) +
+ "_")))
+ comptID_sbml[compt] = csetId
+ if isinstance(compt,moose.EndoMesh):
+ if comptID_sbml.get(compt.surround) == None:
+ createCompt = False
+ return False,groupInfo,"Outer compartment need to be specified for EndoMesh "
+ #return " EndoMesh need to outer compartment to be specified "
+ else:
+ comptAnno = "<moose:CompartmentAnnotation><moose:Mesh>" + \
+ str(compt.className) + "</moose:Mesh>\n" + \
+ "<moose:surround>" + \
+ str(comptID_sbml[compt.surround])+ "</moose:surround>\n" + \
+ "<moose:isMembraneBound>" + \
+ str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" + \
+ "</moose:CompartmentAnnotation>"
+ elif isinstance (compt,moose.CylMesh) :
size = (compt.volume/compt.numDiffCompts)*pow(10,3)
comptAnno = "<moose:CompartmentAnnotation><moose:Mesh>" + \
str(compt.className) + "</moose:Mesh>\n" + \
- "<moose:numDiffCompts>" + \
- str(compt.numDiffCompts)+ "</moose:numDiffCompts>\n" + \
+ "<moose:totLength>" + \
+ str(compt.totLength)+ "</moose:totLength>\n" + \
+ "<moose:diffLength>" + \
+ str(compt.diffLength)+ "</moose:diffLength>\n" + \
+ "<moose:isMembraneBound>" + \
+ str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" + \
"</moose:CompartmentAnnotation>"
- else:
- size = compt.volume * pow(10, 3)
- ndim = compt.numDimensions
- c1 = cremodel_.createCompartment()
- if comptAnno:
- c1.setAnnotation(comptAnno)
- c1.setId(str(idBeginWith(comptName +
- "_" +
- str(compt.getId().value) +
- "_" +
- str(compt.getDataIndex()) +
- "_")))
- c1.setName(comptName)
- c1.setConstant(True)
- c1.setSize(compt.volume*pow(10,3))
- #c1.setSize(size)
- c1.setSpatialDimensions(ndim)
- c1.setUnits('volume')
- #For each compartment get groups information along
- for grp in moose.wildcardFind(compt.path+'/##[0][TYPE=Neutral]'):
- grp_cmpt = findGroup_compt(grp.parent)
- try:
- value = groupInfo[moose.element(grp)]
- except KeyError:
- # Grp is not present
- groupInfo[moose.element(grp)] = []
-
+ else:
+ comptAnno = "<moose:CompartmentAnnotation><moose:Mesh>" + \
+ str(compt.className) + "</moose:Mesh>\n" + \
+ "<moose:isMembraneBound>" + \
+ str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" + \
+ "</moose:CompartmentAnnotation>"
+ if createCompt:
+ c1 = cremodel_.createCompartment()
+ c1.setId(csetId)
+ c1.setName(comptName)
+ c1.setConstant(True)
+ c1.setSize(compt.volume*pow(10,3))
+ #c1.setSize(size)
+ if isinstance(compts,moose.EndoMesh):
+ c1.outside = comptID_sbml[compt.surround]
+
+ if comptAnno:
+ c1.setAnnotation(comptAnno)
+ c1.setSpatialDimensions(ndim)
+ if ndim == 3:
+ c1.setUnits('volume')
+ elif ndim == 2:
+ c1.setUnits('area')
+ elif ndim == 1:
+ c1.setUnits('metre')
+
+ #For each compartment get groups information along
+ for grp in moose.wildcardFind(compt.path+'/##[0][TYPE=Neutral]'):
+ grp_cmpt = findGroup_compt(grp.parent)
+ try:
+ value = groupInfo[moose.element(grp)]
+ except KeyError:
+ # Grp is not present
+ groupInfo[moose.element(grp)] = []
+
if compts:
- return True,groupInfo
+ return True,groupInfo,""
else:
- return False,groupInfo
+ return False,groupInfo,""
# write Simulation runtime,simdt,plotdt
def writeSimulationAnnotation(modelpath):
@@ -1061,7 +1128,9 @@ def writeSimulationAnnotation(modelpath):
ori = q.path
name = convertSpecialChar(q.name)
graphSpefound = False
- while not(isinstance(moose.element(q), moose.CubeMesh) or isinstance(moose.element(q),moose.CylMesh)):
+
+ while not(isinstance(moose.element(q), moose.CubeMesh) or isinstance(moose.element(q),moose.CylMesh) \
+ or isinstance(moose.element(q), moose.EndoMesh) or isinstance(moose.element(q),moose.NeuroMesh)):
q = q.parent
graphSpefound = True
if graphSpefound:
@@ -1076,6 +1145,7 @@ def writeSimulationAnnotation(modelpath):
if plots != " ":
modelAnno = modelAnno + "<moose:plots> " + plots + "</moose:plots>\n"
modelAnno = modelAnno + "</moose:ModelAnnotation>"
+
return modelAnno
def recalculatecoordinates(modelpath, mObjlist,xcord,ycord):
diff --git a/moose-core/python/moose/__init__.py b/moose-core/python/moose/__init__.py
index 407b6950d8246916d0178f6962a7f28bcae4c51c..3c398033985d709c65bdccbbddbcde446198aa24 100644
--- a/moose-core/python/moose/__init__.py
+++ b/moose-core/python/moose/__init__.py
@@ -1,13 +1,18 @@
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
-# Bring everything from moose.py to global namespace.
-from moose.moose import *
+# Use this format in all logger inside logger. Define it before any moose
+# related module is imported.
+LOGGING_FORMAT = '%(asctime)s %(message)s'
# Bring everything from c++ module to global namespace. Not everything is
# imported by the pervios import statement.
from moose._moose import *
+# Bring everything from moose.py to global namespace.
+# IMP: It will overwrite any c++ function with the same name.
+from moose.moose import *
+from moose.server import *
+
# create a shorthand for version() call here.
__version__ = version()
-
diff --git a/moose-core/python/moose/chemMerge/merge.py b/moose-core/python/moose/chemMerge/merge.py
index 6b37ae44d5665752dc1776de9cfeb3e560984717..d3724c8cff0a22ba04d6bcfe1e507730f81f0ccc 100644
--- a/moose-core/python/moose/chemMerge/merge.py
+++ b/moose-core/python/moose/chemMerge/merge.py
@@ -144,17 +144,17 @@ def mergeChemModel(src,des):
poolListinb = {}
poolListinb = updatePoolList(comptBdict)
- R_Duplicated, R_Notcopiedyet,R_Daggling = [], [], []
- E_Duplicated, E_Notcopiedyet,E_Daggling = [], [], []
+ R_Duplicated, R_Notcopiedyet,R_Dangling = [], [], []
+ E_Duplicated, E_Notcopiedyet,E_Dangling = [], [], []
for key in list(dictComptA.keys()):
funcExist, funcNotallowed = [], []
funcExist,funcNotallowed = functionMerge(dictComptB,dictComptA,key)
poolListinb = updatePoolList(dictComptB)
- R_Duplicated,R_Notcopiedyet,R_Daggling = reacMerge(dictComptA,dictComptB,key,poolListinb)
+ R_Duplicated,R_Notcopiedyet,R_Dangling = reacMerge(dictComptA,dictComptB,key,poolListinb)
poolListinb = updatePoolList(dictComptB)
- E_Duplicated,E_Notcopiedyet,E_Daggling = enzymeMerge(dictComptB,dictComptA,key,poolListinb)
+ E_Duplicated,E_Notcopiedyet,E_Dangling = enzymeMerge(dictComptB,dictComptA,key,poolListinb)
# if isinstance(src, str):
# if os.path.isfile(src) == True:
@@ -209,15 +209,15 @@ def mergeChemModel(src,des):
for ed in list(E_Notcopiedyet):
print ("%s " %str(ed.name))
- if R_Daggling or E_Daggling:
- print ("\n Daggling reaction/enzyme are not allowed in moose, these are not merged to %s from %s" %(dfile, sfile))
- if R_Daggling:
+ if R_Dangling or E_Dangling:
+ print ("\n Dangling reaction/enzyme are not allowed in moose, these are not merged to %s from %s" %(dfile, sfile))
+ if R_Dangling:
print("Reaction: ")
- for rd in list(R_Daggling):
+ for rd in list(R_Dangling):
print ("%s " %str(rd.name))
- if E_Daggling:
+ if E_Dangling:
print ("Enzyme:")
- for ed in list(E_Daggling):
+ for ed in list(E_Dangling):
print ("%s " %str(ed.name))
## Model is saved
@@ -436,7 +436,7 @@ def copy_deleteUnlyingPoolObj(pool,path):
poolcopied = moose.copy(pool,path)
copied = True
# deleting function and enzyme which gets copied if exist under pool
- # This is done to ensure daggling function / enzyme not copied.
+ # This is done to ensure Dangling function / enzyme not copied.
funclist = []
for types in ['setConc','setN','increment']:
funclist.extend(moose.element(poolcopied).neighbors[types])
@@ -456,7 +456,7 @@ def updatePoolList(comptAdict):
def enzymeMerge(comptD,comptS,key,poolListind):
war_msg = ""
- RE_Duplicated, RE_Notcopiedyet, RE_Daggling = [], [], []
+ RE_Duplicated, RE_Notcopiedyet, RE_Dangling = [], [], []
comptDpath = moose.element(comptD[key]).path
comptSpath = moose.element(comptS[key]).path
objD = moose.element(comptDpath).parent.name
@@ -501,7 +501,7 @@ def enzymeMerge(comptD,comptS,key,poolListind):
RE_Notcopiedyet.append(es)
else:
# -- it is dagging reaction
- RE_Daggling.append(es)
+ RE_Dangling.append(es)
else:
#Same Enzyme name
# -- Same substrate and product including same volume then don't copy
@@ -551,12 +551,12 @@ def enzymeMerge(comptD,comptS,key,poolListind):
if eSsubname and eSprdname:
RE_Notcopiedyet.append(es)
else:
- RE_Daggling.append(es)
+ RE_Dangling.append(es)
- return RE_Duplicated,RE_Notcopiedyet,RE_Daggling
+ return RE_Duplicated,RE_Notcopiedyet,RE_Dangling
def reacMerge(comptS,comptD,key,poolListina):
- RE_Duplicated, RE_Notcopiedyet, RE_Daggling = [], [], []
+ RE_Duplicated, RE_Notcopiedyet, RE_Dangling = [], [], []
war_msg = ""
comptSpath = moose.element(comptS[key]).path
comptDpath = moose.element(comptD[key]).path
@@ -594,9 +594,9 @@ def reacMerge(comptS,comptD,key,poolListina):
RE_Notcopiedyet.append(rs)
else:
# -- it is dagging reaction
- RE_Daggling.append(rs)
- #print ("This reaction \""+rb.path+"\" has no substrate/product daggling reaction are not copied")
- #war_msg = war_msg+"\nThis reaction \""+rb.path+"\" has no substrate/product daggling reaction are not copied"
+ RE_Dangling.append(rs)
+ #print ("This reaction \""+rb.path+"\" has no substrate/product Dangling reaction are not copied")
+ #war_msg = war_msg+"\nThis reaction \""+rb.path+"\" has no substrate/product Dangling reaction are not copied"
else:
#Same reaction name
@@ -640,9 +640,9 @@ def reacMerge(comptS,comptD,key,poolListina):
if rSsubname and rSprdname:
RE_Notcopiedyet.append(rs)
else:
- RE_Daggling.append(rs)
+ RE_Dangling.append(rs)
- return RE_Duplicated,RE_Notcopiedyet,RE_Daggling
+ return RE_Duplicated,RE_Notcopiedyet,RE_Dangling
def subprdList(reac,subprd):
rtype = moose.element(reac).neighbors[subprd]
diff --git a/moose-core/python/moose/chemUtil/chemConnectUtil.py b/moose-core/python/moose/chemUtil/chemConnectUtil.py
index bbb18ed55eee94434adf5dde60d64db7ccdb5086..9c92e613786c8448f0075ac67bf46cc92e14c05e 100644
--- a/moose-core/python/moose/chemUtil/chemConnectUtil.py
+++ b/moose-core/python/moose/chemUtil/chemConnectUtil.py
@@ -9,7 +9,7 @@ __version__ = "1.0.0"
__maintainer__ = "Harsha Rani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
-__updated__ = "Aug 8 2017"
+__updated__ = "Nov 8 2018"
import moose
import numpy as np
@@ -193,7 +193,7 @@ def countitems(mitems,objtype):
def findCompartment(element):
if element.path == '/':
return moose.element('/')
- elif mooseIsInstance(element, ["CubeMesh", "CylMesh"]):
+ elif mooseIsInstance(element, ["CubeMesh", "CylMesh","EndoMesh","NeuroMesh"]):
return (element)
else:
return findCompartment(moose.element(element.parent))
diff --git a/moose-core/python/moose/genesis/writeKkit.py b/moose-core/python/moose/genesis/writeKkit.py
index 4dc03c076b34ef859a9df055c440283c945aedc6..6227bc0b638f7ec00e61250c5d8169c1a6dcabcf 100644
--- a/moose-core/python/moose/genesis/writeKkit.py
+++ b/moose-core/python/moose/genesis/writeKkit.py
@@ -9,9 +9,14 @@ __version__ = "1.0.0"
__maintainer__ = "Harsha Rani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
-__updated__ = "Oct 23 2018"
+__updated__ = "Dec 08 2018"
# 2018
+# Dec 08: using restoreXreacs from fixXreacs
+# Nov 22: searched for _xfer_ instead of xfer
+# Nov 21: xfer pool are not written and cleaned up if part of Reaction/Enzyme or notes,
+# group are checked under all the mesh
+
# Oct 16: Channels are written back to genesis
# only zeroth element is taken for written back to genesis, this is true for CubeMesh and CylMesh
# 2017
@@ -23,7 +28,8 @@ import re
import moose
from moose.chemUtil.chemConnectUtil import *
from moose.chemUtil.graphUtils import *
-
+from moose.fixXreacs import restoreXreacs
+
foundmatplotlib_ = False
try:
import matplotlib
@@ -71,7 +77,7 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
global cmin,cmax,xmin,xmax,ymin,ymax
cmin, xmin, ymin = 0, 0, 0
cmax, xmax, ymax = 1, 1, 1
-
+ moose.fixXreacs.restoreXreacs(modelpath)
compt = moose.wildcardFind(modelpath+'/##[0][ISA=ChemCompt]')
maxVol = estimateDefaultVol(compt)
positionInfoExist = True
@@ -138,6 +144,7 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
" /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \"edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>\" auto 0.6\n"
"simundump xtext /file/notes 0 1\n")
storeReacMsg(reacList,f)
+
storeEnzMsg(enzList,f)
storeChanMsg(chanList,f)
if tgraphs:
@@ -152,6 +159,7 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
return False
def findMinMax(sceneitems):
+
cmin = 0.0
cmax = 1.0
xmin,xymin = 0.0,0.0
@@ -434,14 +442,18 @@ def trimPath(mobj):
# Any moose object comes under /kinetics then one level down the path is taken.
# e.g /group/poolObject or /Reac
if found:
- if mobj.name != "kinetics" and (mobj.className != "CubeMesh"):
+ if mobj.name != "kinetics":# and ( (mobj.className != "CubeMesh") and (mobj.className != "CylMesh") and (mobj.className != "EndoMesh") and (mobj.className != "NeuroMesh")):
splitpath = original.path[(original.path.find(mobj.name)):len(original.path)]
else:
pos = original.path.find(mobj.name)
+ #ss = re.compile(r'\b%s\b' %mobj.name)
+ #a = re.search(ss, original.path)
+ #pos = a.start()
slash = original.path.find('/',pos+1)
splitpath = original.path[slash+1:len(original.path)]
splitpath = re.sub("\[[0-9]+\]", "", splitpath)
s = splitpath.replace("_dash_",'-')
+ s = splitpath.replace("_space_","_")
return s
# def writeSumtotal( modelpath,f):
@@ -619,7 +631,6 @@ def writePool(modelpath,f,volIndex,sceneitems):
color = getRandColor()
if textcolor == "" or textcolor == " ":
textcolor = getRandColor()
-
f.write("simundump kpool /kinetics/" + trimPath(p) + " 0 " +
str(p.diffConst) + " " +
str(0) + " " +
@@ -696,13 +707,17 @@ def writeCompartment(modelpath,compts,f):
i = i+1
x = xmin+4
y = ymax+1
+ #geometryname = compt.name
if vecIndex > 0:
geometry = geometry+"simundump geometry /kinetics" + "/geometry[" + str(vecIndex) +"] 0 " + str(size) + " " + str(ndim) + " sphere " +" \"\" white black "+ str(int(x)) + " " +str(int(y)) +" 0\n";
volIndex[float(size)] = "/geometry["+str(vecIndex)+"]"
+ #geometry = geometry+"simundump geometry /kinetics/" + str(geometryname) + " " +str(size) + " " + str(ndim) + " sphere " +" \"\" white black " + str(int(x)) + " "+str(int(y))+ " 0\n";
+ #volIndex[float(size)] = geometryname
else:
-
+ #geometry = geometry+"simundump geometry /kinetics/" + str(geometryname) + " " + str(size) + " " + str(ndim) + " sphere " +" \"\" white black " + str(int(x)) + " "+str(int(y))+ " 0\n";
geometry = geometry+"simundump geometry /kinetics" + "/geometry 0 " + str(size) + " " + str(ndim) + " sphere " +" \"\" white black " + str(int(x)) + " "+str(int(y))+ " 0\n";
volIndex[float(size)] = "/geometry"
+ #volIndex[float(size)] = geometryname
f.write(geometry)
writeGroup(modelpath,f)
return volIndex
@@ -787,11 +802,12 @@ def writeNotes(modelpath,f):
moose.wildcardFind(modelpath+"/##[0][ISA=Function]") +\
moose.wildcardFind(modelpath+"/##[0][ISA=StimulusTable]")
for item in items:
- if moose.exists(item.path+'/info'):
- info = item.path+'/info'
- notes = moose.Annotator(info).getField('notes')
- if (notes):
- f.write("call /kinetics/"+ trimPath(item)+"/notes LOAD \ \n\""+moose.Annotator(info).getField('notes')+"\"\n")
+ if not re.search("xfer",item.name):
+ if moose.exists(item.path+'/info'):
+ info = item.path+'/info'
+ notes = moose.Annotator(info).getField('notes')
+ if (notes):
+ f.write("call /kinetics/"+ trimPath(item)+"/notes LOAD \ \n\""+moose.Annotator(info).getField('notes')+"\"\n")
def writeFooter1(f):
f.write("\nenddump\n // End of dump\n")
diff --git a/moose-core/python/moose/moose.py b/moose-core/python/moose/moose.py
index a55bc7be1f1c6b86d36b838d68a7be7b9e245d17..c3c6b60db6cf3de1c49cd6d2e5516d7bc2b91d22 100644
--- a/moose-core/python/moose/moose.py
+++ b/moose-core/python/moose/moose.py
@@ -1,20 +1,17 @@
# -*- coding: utf-8 -*-
-from __future__ import print_function, division, absolute_import
-
# Author: Subhasis Ray
# Maintainer: Dilawar Singh, Harsha Rani, Upi Bhalla
+from __future__ import print_function, division, absolute_import
import warnings
+import os
import pydoc
-import moose
-import moose.utils as mu
from io import StringIO
-from os.path import splitext
from contextlib import closing
# Import function from C++ module into moose namespace.
-# from moose._moose import *
import moose._moose as _moose
+import moose.utils as mu
# sbml import.
sbmlImport_, sbmlError_ = True, ''
@@ -60,40 +57,58 @@ except Exception as e:
mergechemImport_ = False
mergechemError_ = '%s' % e
-def loadModel(filename, target,method=None):
- solverClass = 'Neutral'
- if method != None:
- solverClass = method
- try:
- f = open(filename,'r')
- f.close()
- except IOError as e:
- print (e)
- return
- else:
- file_name,extension = splitext(filename)
- if extension in [".swc",".p"]:
- ret = moose._moose.loadModel(filename,target,"Neutral")
- elif extension in [".g",".cspace"]:
- #only if genesis or cspace file, then mooseAddChemSolver is called
- ret = moose._moose.loadModel(filename,target,"ee")
-
+def loadModel(filename, modelpath, solverclass="gsl"):
+ """loadModel: 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.
+ method: str
+ solver type to be used for simulating the model.
+ TODO: Link to detailed description of solvers?
+
+ Returns
+ -------
+ object
+ moose.element if succcessful else None.
+ """
+
+ if not os.path.isfile( os.path.realpath(filename) ):
+ mu.warn( "Model file '%s' does not exists or is not readable." % filename )
+ return None
+
+ extension = os.path.splitext(filename)[1]
+ if extension in [".swc", ".p"]:
+ return _moose.loadModelInternal(filename, modelpath, "Neutral" )
+
+ if extension in [".g", ".cspace"]:
+ # only if genesis or cspace file and method != ee then only
+ # mooseAddChemSolver is called.
+ ret = _moose.loadModelInternal(filename, modelpath, "ee")
+ sc = solverclass.lower()
+ if sc in ["gssa","gillespie","stochastic","gsolve"]:
+ method = "gssa"
+ elif sc in ["gsl","runge kutta","deterministic","ksolve","rungekutta","rk5","rkf","rk"]:
+ method = "gsl"
+ elif sc in ["exponential euler","exponentialeuler","neutral"]:
+ method = "ee"
+ else:
method = "ee"
- if solverClass.lower() in ["gssa","gillespie","stochastic","gsolve"]:
- method = "gssa"
- elif solverClass.lower() in ["gsl","runge kutta","deterministic","ksolve","rungekutta","rk5","rkf","rk"]:
- method = "gsl"
- elif solverClass.lower() in ["exponential euler","exponentialeuler","neutral"]:
- method = "ee"
-
- if method != 'ee':
- chemError_ = _chemUtil.add_Delete_ChemicalSolver.mooseAddChemSolver(target,method)
+
+ if method != 'ee':
+ chemError = _chemUtil.add_Delete_ChemicalSolver.mooseAddChemSolver(modelpath, method)
return ret
+ else:
+ mu.error( "Unknown model extenstion '%s'" % extension)
+ return None
# Version
def version( ):
# Show user version.
- return moose._moose.VERSION
+ return _moose.VERSION
# Tests
from moose.moose_test import test
@@ -125,36 +140,42 @@ known_types = ['void',
def mooseReadSBML(filepath, loadpath, solver='ee',validate="on"):
"""Load SBML model.
- keyword arguments: \n
-
- filepath -- filepath to be loaded \n
- loadpath -- Root path for this model e.g. /model/mymodel \n
- solver -- Solver to use (default 'ee' ) \n
-
+ Parameter
+ --------
+ filepath: str
+ filepath to be loaded.
+ loadpath : str
+ Root path for this model e.g. /model/mymodel
+ solver : str
+ Solver to use (default 'ee').
+ Available options are "ee", "gsl", "stochastic", "gillespie"
+ "rk", "deterministic"
+ For full list see ??
"""
global sbmlImport_
if sbmlImport_:
- return _readSBML.mooseReadSBML( filepath, loadpath, solver,validate )
+ return _readSBML.mooseReadSBML(filepath, loadpath, solver, validate)
else:
print( sbmlError_ )
return False
-
def mooseWriteSBML(modelpath, filepath, sceneitems={}):
- """Writes loaded model under modelpath to a file in SBML format.
-
- keyword arguments:\n
-
- modelpath -- model path in moose e.g /model/mymodel \n
- filepath -- Path of output file. \n
- sceneitems -- dictlist (UserWarning: user need not worry about this) \n
- layout position is saved in Annotation field of all the moose Object (pool,Reaction,enzyme)\n
- If this function is called from \n
- -- GUI, the layout position of moose object is passed \n
- -- command line, \n
- ---if genesis/kkit model is loaded then layout position is taken from the file \n
- --- else, auto-coordinates is used for layout position and passed
-
+ """mooseWriteSBML: Writes loaded model under modelpath to a file in SBML format.
+
+ Parameters
+ ----------
+ modelpath : str
+ model path in moose e.g /model/mymodel \n
+ filepath : str
+ Path of output file. \n
+ sceneitems : dict
+ UserWarning: user need not worry about this layout position is saved in
+ Annotation field of all the moose Object (pool,Reaction,enzyme).
+ If this function is called from
+ * GUI - the layout position of moose object is passed
+ * command line - NA
+ * if genesis/kkit model is loaded then layout position is taken from the file
+ * otherwise auto-coordinates is used for layout position.
"""
if sbmlImport_:
return _writeSBML.mooseWriteSBML(modelpath, filepath, sceneitems)
@@ -163,13 +184,15 @@ def mooseWriteSBML(modelpath, filepath, sceneitems={}):
return False
-def mooseWriteKkit(modelpath, filepath,sceneitems={}):
+def mooseWriteKkit(modelpath, filepath, sceneitems={}):
"""Writes loded model under modelpath to a file in Kkit format.
- keyword arguments:\n
-
- modelpath -- model path in moose \n
- filepath -- Path of output file.
+ Parameters
+ ----------
+ modelpath : str
+ Model path in moose.
+ filepath : str
+ Path of output file.
"""
global kkitImport_, kkitImport_err_
if not kkitImport_:
@@ -180,10 +203,14 @@ def mooseWriteKkit(modelpath, filepath,sceneitems={}):
def mooseDeleteChemSolver(modelpath):
- """ deletes solver on all the compartment and its children.
- This is neccesary while created a new moose object on a pre-existing modelpath,\n
- this should be followed by mooseAddChemSolver for add solvers on to compartment to simulate else
- default is Exponential Euler (ee)
+ """mooseDeleteChemSolver
+ deletes solver on all the compartment and its children.
+
+ Notes
+ -----
+ This is neccesary while created a new moose object on a pre-existing modelpath,
+ this should be followed by mooseAddChemSolver for add solvers on to compartment
+ to simulate else default is Exponential Euler (ee)
"""
if chemImport_:
return _chemUtil.add_Delete_ChemicalSolver.mooseDeleteChemSolver(modelpath)
@@ -193,15 +220,17 @@ def mooseDeleteChemSolver(modelpath):
def mooseAddChemSolver(modelpath, solver):
- """ Add solver on chemical compartment and its children for calculation
-
- keyword arguments:\n
+ """mooseAddChemSolver:
+ Add solver on chemical compartment and its children for calculation
- modelpath -- model path that is loaded into moose \n
- solver -- "Exponential Euler" (ee) (default), \n
- "Gillespie" ("gssa"), \n
- "Runge Kutta" ("gsl")
+ Parameters
+ ----------
+ modelpath : str
+ Model path that is loaded into moose.
+ solver : str
+ Exponential Euler "ee" is default. Other options are Gillespie ("gssa"),
+ Runge Kutta ("gsl") etc. Link to documentation?
"""
if chemImport_:
chemError_ = _chemUtil.add_Delete_ChemicalSolver.mooseAddChemSolver(modelpath, solver)
@@ -211,9 +240,8 @@ def mooseAddChemSolver(modelpath, solver):
return False
def mergeChemModel(src, des):
- """ Merges two chemical model, \n
- File or filepath can be passed
- source is merged to destination
+ """mergeChemModel: Merges two chemical model.
+ File or filepath can be passed source is merged to destination
"""
#global mergechemImport_
if mergechemImport_:
@@ -281,7 +309,6 @@ def le(el=None):
ce = _moose.setCwe # ce is a GENESIS shorthand for change element.
-
def syncDataHandler(target):
"""Synchronize data handlers for target.
@@ -360,7 +387,6 @@ def showfield(el, field='*', showtype=False):
def showfields(el, showtype=False):
"""Convenience function. Should be deprecated if nobody uses it.
-
"""
warnings.warn(
'Deprecated. Use showfield(element, field="*", showtype=True) instead.',
@@ -374,7 +400,6 @@ finfotypes = [('valueFinfo', 'value field'),
('sharedFinfo', 'shared message field'),
('lookupFinfo', 'lookup field')]
-
def listmsg(el):
"""Return a list containing the incoming and outgoing messages of
`el`.
@@ -627,7 +652,3 @@ def doc(arg, inherited=True, paged=True):
pager(text)
else:
print(text)
-
-
-#
-# moose.py ends here
diff --git a/moose-core/python/moose/neuroml2/reader.py b/moose-core/python/moose/neuroml2/reader.py
index 2f2e2d85c8c35c5b227b5e436fd4c39c26521409..1629e6de7a3eaa73d574a42ea0a6a4f81103b631 100644
--- a/moose-core/python/moose/neuroml2/reader.py
+++ b/moose-core/python/moose/neuroml2/reader.py
@@ -1,37 +1,71 @@
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
-# reader.py ---
-#
-# Filename: reader.py
-# Description:
+# Description: NeuroML2 reader.
+# Implementation of reader for NeuroML 2 models.
+# TODO: handle morphologies of more than one segment...
# Author: Subhasis Ray, Padraig Gleeson
-# Maintainer:
+# Maintainer: Dilawar Singh <dilawars@ncbs.res.in>
# Created: Wed Jul 24 15:55:54 2013 (+0530)
-# Version:
-# Last-Updated: 15 Jan 2018, pgleeson
-# 16 Jan 2018, dilawar, python3 compatible imports.
-#
+# Notes:
+# For update/log, please see git-blame documentation or browse the github
+# repo https://github.com/BhallaLab/moose-core
-"""Implementation of reader for NeuroML 2 models.
-TODO: handle morphologies of more than one segment...
-"""
try:
from future_builtins import zip, map
-except ImportError:
+except ImportError as e:
pass
-import sys
import os
import math
import numpy as np
-import neuroml as nml
-from pyneuroml import pynml
import moose
-import moose.utils as mu
-from .units import SI
+import logging
+logging.basicConfig( format=moose.LOGGING_FORMAT )
+logger_ = logging.getLogger(__name__)
+
+import moose
+import neuroml as nml
+import pyneuroml.pynml as pynml
+from moose.neuroml2.units import SI
+
+def _write_flattened_nml( doc, outfile ):
+ """_write_flattened_nml
+ Concat all NML2 read by moose and generate one flattened NML file.
+ Only useful when debugging.
+
+ :param doc: NML document (nml.doc)
+ :param outfile: Name of the output file.
+ """
+ import neuroml.writers
+ neuroml.writers.NeuroMLWriter.write( doc, outfile )
+ logger_.debug( "Wrote flattened NML model to %s" % outfile )
+
+def _gates_sorted( all_gates ):
+ """_gates_sorted
+
+ Parameters
+ ----------
+ all_gates (list)
+ List of all moose.HHChannel.gates
+
+ Notes
+ -----
+ If the id of gates are subset of 'x', 'y' or 'z' then sort them so they load in
+ X, Y or Z gate respectively. Otherwise do not touch them i.e. first gate
+ will be loaded into X, second into Y and so on.
+ """
+ allMooseGates = ['x', 'y', 'z']
+ allGatesDict = { g.id : g for g in all_gates }
+ gateNames = [ g.id.lower() for g in all_gates ]
+ if set(gateNames).issubset(set(allMooseGates)):
+ sortedGates = []
+ for gid in allMooseGates:
+ sortedGates.append( allGatesDict.get(gid) )
+ return sortedGates
+ return all_gates
def _unique( ls ):
res = [ ]
@@ -40,31 +74,58 @@ def _unique( ls ):
res.append( l )
return res
-def sarea(comp):
- """
- Return the surface area of compartment from length and
- diameter.
+def _isConcDep(ct):
+ """_isConcDep
+ Check if componet is dependant on concentration. Most HHGates are
+ dependant on voltage.
- Parameters
- ----------
- comp : Compartment instance.
+ :param ct: ComponentType
+ :type ct: nml.ComponentType
+
+ :return: True if Component is depenant on conc, False otherwise.
+ """
+ if 'ConcDep' in ct.extends:
+ return True
+ return False
+
+def _findCaConcVariableName():
+ """_findCaConcVariableName
+ Find a suitable CaConc for computing HHGate tables.
+ This is a hack, though it is likely to work in most cases.
+ """
+ caConcs = moose.wildcardFind( '/library/##[TYPE=CaConc]' )
+ assert len(caConcs) >= 1, "No moose.CaConc found. Currently moose \
+ supports HHChannel which depends only on moose.CaConc ."
+ return caConcs[0].name
- Returns
- -------
- s : float
- surface area of `comp`.
+def sarea(comp):
+ """sarea
+ Return the surface area (2Ï–rL) of compartment from length and diameter.
+ :param comp: Compartment instance.
+ :type comp: str
+ :return: surface area of `comp`.
+ :rtype: float
"""
if comp.length > 0:
- return comp.length * comp.diameter * np.pi
+ return math.pi * comp.diameter * comp.length
else:
- return comp.diameter * comp.diameter * np.pi
+ return math.pi * comp.diameter * comp.diameter
-def xarea(comp):
+def xarea(compt):
+ """xarea
+ Return the cross sectional area (ðœ‹r²) from the diameter of the compartment.
+
+ Note:
+ ----
+ How to do it for spherical compartment?
+
+ :param compt: Compartment in moose.
+ :type compt: moose.Compartment
+ :return: cross sectional area.
+ :rtype: float
"""
- Return the cross sectional area from diameter of the
- compartment. How to do it for spherical compartment?"""
- return comp.diameter * comp.diameter * np.pi / 4.0
+ return math.pi * (compt.diameter/2.0)**2.0
def setRa(comp, resistivity):
"""Calculate total raxial from specific value `resistivity`"""
@@ -81,7 +142,6 @@ def setEk(comp, erev):
"""Set reversal potential"""
comp.setEm(erev)
-
def getSegments(nmlcell, component, sg_to_segments):
"""Get the list of segments the `component` is applied to"""
sg = component.segment_groups
@@ -109,8 +169,11 @@ class NML2Reader(object):
creates a passive neuronal morphology `/library/Purk2M9s`.
"""
def __init__(self, verbose=False):
+ global logger_
self.lunit = 1e-6 # micron is the default length unit
self.verbose = verbose
+ if self.verbose:
+ logger_.setLevel( logging.DEBUG )
self.doc = None
self.filename = None
self.nml_to_moose = {} # NeuroML object to MOOSE object
@@ -119,9 +182,11 @@ class NML2Reader(object):
self.proto_chans = {} # map id to prototype channels in moose
self.proto_pools = {} # map id to prototype pools (Ca2+, Mg2+)
self.includes = {} # Included files mapped to other readers
- self.lib = moose.Neutral('/library')
+ self.lib = moose.element('/library') if moose.exists('/library') \
+ else moose.Neutral( '/library' )
self.id_to_ionChannel = {}
self._cell_to_sg = {} # nml cell to dict - the dict maps segment groups to segments
+ self._variables = {}
self.cells_in_populations = {}
self.pop_to_cell_type = {}
@@ -134,27 +199,26 @@ class NML2Reader(object):
self.doc = nml.loaders.read_neuroml2_file(
filename, include_includes=True, verbose=self.verbose)
- if self.verbose:
- mu.info('Parsed NeuroML2 file: %s'% filename)
self.filename = filename
+
+ logger_.info('Parsed NeuroML2 file: %s'% filename)
+ if self.verbose:
+ _write_flattened_nml( self.doc, '%s__flattened.xml' % self.filename )
if len(self.doc.networks)>=1:
self.network = self.doc.networks[0]
moose.celsius = self._getTemperature()
-
self.importConcentrationModels(self.doc)
self.importIonChannels(self.doc)
self.importInputs(self.doc)
-
for cell in self.doc.cells:
self.createCellPrototype(cell, symmetric=symmetric)
if len(self.doc.networks)>=1:
self.createPopulations()
self.createInputs()
- mu.info("Read all from %s"%filename)
def _getTemperature(self):
if self.network is not None:
@@ -179,7 +243,7 @@ class NML2Reader(object):
mpop = moose.element(ep) if moose.exists(ep) else moose.Neutral(ep)
self.cells_in_populations[pop.id] ={}
for i in range(pop.size):
- mu.info("Creating %s/%s instances of %s under %s"%(i,pop.size,pop.component, mpop))
+ logger_.info("Creating %s/%s instances of %s under %s"%(i,pop.size,pop.component, mpop))
self.pop_to_cell_type[pop.id]=pop.component
chid = moose.copy(self.proto_cells[pop.component], mpop, '%s'%(i))
self.cells_in_populations[pop.id][i]=chid
@@ -302,7 +366,7 @@ class NML2Reader(object):
according to NeuroML2 cell `nmlcell`."""
bp = nmlcell.biophysical_properties
if bp is None:
- mu.info('Warning: %s in %s has no biophysical properties' % (nmlcell.id, self.filename))
+ logger_.info('Warning: %s in %s has no biophysical properties' % (nmlcell.id, self.filename))
return
self.importMembraneProperties(nmlcell, moosecell, bp.membrane_properties)
self.importIntracellularProperties(nmlcell, moosecell, bp.intracellular_properties)
@@ -310,7 +374,7 @@ class NML2Reader(object):
def importMembraneProperties(self, nmlcell, moosecell, mp):
"""Create the membrane properties from nmlcell in moosecell"""
if self.verbose:
- mu.info('Importing membrane properties')
+ logger_.info('Importing membrane properties')
self.importCapacitances(nmlcell, moosecell, mp.specific_capacitances)
self.importChannelsToCell(nmlcell, moosecell, mp)
self.importInitMembPotential(nmlcell, moosecell, mp)
@@ -338,8 +402,12 @@ class NML2Reader(object):
def importSpecies(self, nmlcell, properties):
sg_to_segments = self._cell_to_sg[nmlcell]
for species in properties.species:
- if (species.concentration_model is not None) and \
- (species.concentration_model.id not in self.proto_pools):
+ # Developer note: Not sure if species.concentration_model should be
+ # a nml element of just plain string. I was getting plain text from
+ # nml file here.
+ concModel = species.concentration_model
+ if (concModel is not None) and (concModel not in self.proto_pools):
+ logger_.warn("No concentrationModel '%s' found."%concModel)
continue
segments = getSegments(nmlcell, species, sg_to_segments)
for seg in segments:
@@ -350,22 +418,23 @@ class NML2Reader(object):
"""Copy the prototype pool `species` to compartment. Currently only
decaying pool of Ca2+ supported"""
proto_pool = None
- if species.concentrationModel in self.proto_pools:
- proto_pool = self.proto_pools[species.concentration_model]
+ concModel = species.concentration_model
+ if concModel in self.proto_pools:
+ proto_pool = self.proto_pools[concModel]
else:
for innerReader in self.includes.values():
- if species.concentrationModel in innerReader.proto_pools:
- proto_pool = innerReader.proto_pools[species.concentrationModel]
+ if concModel in innerReader.proto_pools:
+ proto_pool = innerReader.proto_pools[concModel]
break
if not proto_pool:
- raise Exception('No prototype pool for %s referred to by %s' % (
- species.concentration_model, species.id)
- )
+ msg = 'No prototype pool for %s referred to by %s' % (concModel, species.id)
+ logger_.error(msg)
+ raise RuntimeError(msg)
pool_id = moose.copy(proto_pool, compartment, species.id)
pool = moose.element(pool_id)
pool.B = pool.B / (np.pi * compartment.length * (
- 0.5 * compartment.diameter + pool.thickness) *
- (0.5 * compartment.diameter - pool.thickness)
+ 0.5 * compartment.diameter + pool.thick) *
+ (0.5 * compartment.diameter - pool.thick)
)
return pool
@@ -383,40 +452,56 @@ class NML2Reader(object):
if hasattr(chan,'gates'):
return len(chan.gate_hh_rates)+len(chan.gates)==0
return False
-
+ def evaluate_moose_component(self, ct, variables):
+ print( "[INFO ] Not implemented." )
+ return False
+
def calculateRateFn(self, ratefn, vmin, vmax, tablen=3000, vShift='0mV'):
"""Returns A / B table from ngate."""
from . import hhfit
+
rate_fn_map = {
'HHExpRate': hhfit.exponential2,
'HHSigmoidRate': hhfit.sigmoid2,
'HHSigmoidVariable': hhfit.sigmoid2,
- 'HHExpLinearRate': hhfit.linoid2 }
+ 'HHExpLinearRate': hhfit.linoid2
+ }
tab = np.linspace(vmin, vmax, tablen)
if self._is_standard_nml_rate(ratefn):
midpoint, rate, scale = map(SI, (ratefn.midpoint, ratefn.rate, ratefn.scale))
return rate_fn_map[ratefn.type](tab, rate, scale, midpoint)
- else:
- for ct in self.doc.ComponentType:
- if ratefn.type == ct.name:
- mu.info("Using %s to evaluate rate"%ct.name)
- rate = []
- for v in tab:
- req_vars = {'v':'%sV'%v,'vShift':vShift,'temperature':self._getTemperature()}
- vals = pynml.evaluate_component(ct, req_variables = req_vars)
- if 'x' in vals:
- rate.append(vals['x'])
- if 't' in vals:
- rate.append(vals['t'])
- if 'r' in vals:
- rate.append(vals['r'])
- return np.array(rate)
+
+ for ct in self.doc.ComponentType:
+ if ratefn.type != ct.name:
+ continue
+
+ logger_.info("Using %s to evaluate rate"%ct.name)
+ rate = []
+ for v in tab:
+ # Note: MOOSE HHGate are either voltage of concentration
+ # dependant. Here we figure out if nml description of gate is
+ # concentration dependant or note.
+ if _isConcDep(ct):
+ # Concentration dependant. Concentration can't be negative.
+ # Find a suitable CaConc from the /library. Currently on Ca
+ # dependant channels are allowed.
+ caConcName = _findCaConcVariableName()
+ req_vars = {caConcName:'%g'%max(0,v),'vShift':vShift,'temperature':self._getTemperature()}
+ else:
+ req_vars = {'v':'%sV'%v,'vShift':vShift,'temperature':self._getTemperature()}
+ req_vars.update( self._variables )
+ vals = pynml.evaluate_component(ct, req_variables=req_vars)
+ v = vals.get('x', vals.get('t', vals.get('r', None)))
+ if v is not None:
+ rate.append(v)
+ return np.array(rate)
print( "[WARN ] Could not determine rate: %s %s %s" %(ratefn.type,vmin,vmax))
return np.array([])
+
def importChannelsToCell(self, nmlcell, moosecell, membrane_properties):
sg_to_segments = self._cell_to_sg[nmlcell]
for chdens in membrane_properties.channel_densities + membrane_properties.channel_density_v_shifts:
@@ -426,17 +511,17 @@ class NML2Reader(object):
try:
ionChannel = self.id_to_ionChannel[chdens.ion_channel]
except KeyError:
- mu.info('No channel with id: %s' % chdens.ion_channel)
+ logger_.info('No channel with id: %s' % chdens.ion_channel)
continue
if self.verbose:
- mu.info('Setting density of channel %s in %s to %s; erev=%s (passive: %s)'%(
+ logger_.info('Setting density of channel %s in %s to %s; erev=%s (passive: %s)'%(
chdens.id, segments, condDensity,erev,self.isPassiveChan(ionChannel))
)
if self.isPassiveChan(ionChannel):
for seg in segments:
- comp = self.nml_to_moose[seg]
+ # comp = self.nml_to_moose[seg]
setRm(self.nml_to_moose[seg], condDensity)
setEk(self.nml_to_moose[seg], erev)
else:
@@ -462,14 +547,14 @@ class NML2Reader(object):
raise Exception('No prototype channel for %s referred to by %s' % (chdens.ion_channel, chdens.id))
if self.verbose:
- mu.info('Copying %s to %s, %s; erev=%s'%(chdens.id, comp, condDensity, erev))
+ logger_.info('Copying %s to %s, %s; erev=%s'%(chdens.id, comp, condDensity, erev))
orig = chdens.id
chid = moose.copy(proto_chan, comp, chdens.id)
chan = moose.element(chid)
for p in self.paths_to_chan_elements.keys():
pp = p.replace('%s/'%chdens.ion_channel,'%s/'%orig)
self.paths_to_chan_elements[pp] = self.paths_to_chan_elements[p].replace('%s/'%chdens.ion_channel,'%s/'%orig)
- #mu.info(self.paths_to_chan_elements)
+ #logger_.info(self.paths_to_chan_elements)
chan.Gbar = sarea(comp) * condDensity
chan.Ek = erev
moose.connect(chan, 'channel', comp, 'channel')
@@ -487,16 +572,21 @@ class NML2Reader(object):
assert len(chan.gate_hh_rates)<=3, "We handle only up to 3 gates in HHCHannel"
if self.verbose:
- mu.info('== Creating channel: %s (%s) -> %s (%s)'%(chan.id, chan.gate_hh_rates, mchan, mgates))
+ logger_.info('== Creating channel: %s (%s) -> %s (%s)'%(chan.id, chan.gate_hh_rates, mchan, mgates))
all_gates = chan.gates + chan.gate_hh_rates
- for ngate, mgate in zip(all_gates,mgates):
+
+ # Sort all_gates such that they come in x, y, z order.
+ all_gates = _gates_sorted( all_gates )
+ for ngate, mgate in zip(all_gates, mgates):
+ if ngate is None:
+ continue
if mgate.name.endswith('X'):
mchan.Xpower = ngate.instances
elif mgate.name.endswith('Y'):
mchan.Ypower = ngate.instances
elif mgate.name.endswith('Z'):
- mchan.Zpower = ngate.instance
+ mchan.Zpower = ngate.instances
mgate.min = vmin
mgate.max = vmax
mgate.divs = vdivs
@@ -524,10 +614,9 @@ class NML2Reader(object):
ngate.q10_settings.type,ngate.q10_settings)
)
- if self.verbose:
- mu.info(' === Gate: %s; %s; %s; %s; %s; scale=%s'% (
- ngate.id, mgate.path, mchan.Xpower, fwd, rev, q10_scale)
- )
+ logger_.debug('+ Gate: %s; %s; %s; %s; %s; scale=%s'% (
+ ngate.id, mgate.path, mchan.Xpower, fwd, rev, q10_scale)
+ )
if (fwd is not None) and (rev is not None):
alpha = self.calculateRateFn(fwd, vmin, vmax, vdivs)
@@ -555,8 +644,7 @@ class NML2Reader(object):
mgate.tableA = q10_scale * (inf / tau)
mgate.tableB = q10_scale * (1 / tau)
- if self.verbose:
- mu.info('%s: Created %s for %s'%(self.filename,mchan.path,chan.id))
+ logger_.info('%s: Created %s for %s'%(self.filename,mchan.path,chan.id))
return mchan
def createPassiveChannel(self, chan):
@@ -565,8 +653,7 @@ class NML2Reader(object):
mchan = moose.element(epath)
else:
mchan = moose.Leakage(epath)
- if self.verbose:
- mu.info('%s: Created %s for %s'%(self.filename,mchan.path,chan.id))
+ logger_.info('%s: Created %s for %s'%(self.filename,mchan.path,chan.id))
return mchan
def importInputs(self, doc):
@@ -586,8 +673,7 @@ class NML2Reader(object):
def importIonChannels(self, doc, vmin=-150e-3, vmax=100e-3, vdivs=5000):
- if self.verbose:
- mu.info('%s: Importing the ion channels' % self.filename )
+ logger_.info('%s: Importing the ion channels' % self.filename )
for chan in doc.ion_channel+doc.ion_channel_hhs:
if chan.type == 'ionChannelHH':
@@ -600,8 +686,7 @@ class NML2Reader(object):
self.id_to_ionChannel[chan.id] = chan
self.nml_to_moose[chan] = mchan
self.proto_chans[chan.id] = mchan
- if self.verbose:
- mu.info( self.filename + ': Created ion channel %s for %s %s'%(
+ logger_.info(self.filename + ': Created ion channel %s for %s %s'%(
mchan.path, chan.type, chan.id))
def importConcentrationModels(self, doc):
@@ -610,18 +695,19 @@ class NML2Reader(object):
def createDecayingPoolConcentrationModel(self, concModel):
"""Create prototype for concentration model"""
- if concModel.name is not None:
+ if hasattr(concModel, 'name') and concModel.name is not None:
name = concModel.name
else:
name = concModel.id
- ca = moose.CaConc('%s/%s' % (self.lib.path, id))
- ca.CaBasal = SI(concModel.restingConc)
- ca.tau = SI(concModel.decayConstant)
- ca.thick = SI(concModel.shellThickness)
+
+ ca = moose.CaConc('%s/%s' % (self.lib.path, name))
+ ca.CaBasal = SI(concModel.resting_conc)
+ ca.tau = SI(concModel.decay_constant)
+ ca.thick = SI(concModel.shell_thickness)
ca.B = 5.2e-6 # B = 5.2e-6/(Ad) where A is the area of the
# shell and d is thickness - must divide by
# shell volume when copying
self.proto_pools[concModel.id] = ca
- self.nml_to_moose[concModel.id] = ca
+ self.nml_to_moose[name] = ca
self.moose_to_nml[ca] = concModel
- mu.debug('Created moose element: %s for nml conc %s' % (ca.path, concModel.id))
+ logger_.debug('Created moose element: %s for nml conc %s' % (ca.path, concModel.id))
diff --git a/moose-core/python/moose/neuroml2/units.py b/moose-core/python/moose/neuroml2/units.py
index 795129a51377b232354eb480ebe0ab898074483c..b85bf6f7912070f3c60c5eed8d28f6bef289e72e 100644
--- a/moose-core/python/moose/neuroml2/units.py
+++ b/moose-core/python/moose/neuroml2/units.py
@@ -1,56 +1,13 @@
# -*- coding: utf-8 -*-
-# units.py ---
-#
-# Filename: units.py
-# Description:
-# Author:
-# Maintainer:
-# Created: Thu Jul 25 16:30:14 2013 (+0530)
-# Version:
-# Last-Updated: Sat Mar 5 14:56:35 2016 (-0500)
-# By: subha
-# Update #: 57
-# 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:
-
-"""Utility to create mapping from NeuroML2 unit strings (as specified
+"""
+Utility to create mapping from NeuroML2 unit strings (as specified
in NeuroMLCoreDimensions.xml) to SI
+Author:
+ Subhasis Ray (Please check commit history for more details).
"""
-from __future__ import print_function
+
+from __future__ import print_function, division
import os
import re
from xml.etree import ElementTree
diff --git a/moose-core/python/moose/server.py b/moose-core/python/moose/server.py
new file mode 100644
index 0000000000000000000000000000000000000000..400058a39e6b21c2d4cbee6de296046d4d940abd
--- /dev/null
+++ b/moose-core/python/moose/server.py
@@ -0,0 +1,320 @@
+# -*- coding: utf-8 -*-
+from __future__ import print_function, division
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2019, Dilawar Singh"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+import sys
+import re
+import os
+import time
+import shutil
+import socket
+import signal
+import tarfile
+import tempfile
+import threading
+import datetime
+import subprocess
+import logging
+
+# setup environment variables for the streamer starts working.
+os.environ['MOOSE_SOCKET_STREAMER_ADDRESS'] = 'ghevar.ncbs.res.in:31416'
+
+# create a logger for this server.
+logging.basicConfig(
+ level=logging.DEBUG,
+ format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
+ datefmt='%m-%d %H:%M',
+ filename='moose_server.log',
+ filemode='a'
+ )
+console = logging.StreamHandler()
+console.setLevel(logging.INFO)
+formatter = logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s')
+console.setFormatter(formatter)
+_logger = logging.getLogger('')
+_logger.addHandler(console)
+
+__all__ = [ 'serve' ]
+
+stop_all_ = False
+
+def handler(signum, frame):
+ global stop_all_
+ _logger.info( "User terminated all processes." )
+ stop_all_ = True
+
+signal.signal( signal.SIGINT, handler)
+
+def split_data( data ):
+ prefixLenght = 10
+ return data[:prefixLenght].strip(), data[prefixLenght:]
+
+def execute(cmd):
+ popen = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+ for stdout_line in iter(popen.stdout.readline, ""):
+ yield stdout_line
+ popen.stdout.close()
+ return_code = popen.wait()
+ if return_code:
+ raise subprocess.CalledProcessError(return_code, cmd)
+
+def send_msg(msg, conn):
+ if not msg.strip():
+ return False
+ _logger.debug( msg )
+ msg = '%s>>> %s' % (socket.gethostname(), msg)
+ conn.sendall( b'%010d%s' % (len(msg), msg))
+
+def run(cmd, conn, cwd=None):
+ oldCWD = os.getcwd()
+ if cwd is not None:
+ os.chdir(cwd)
+ _logger.debug( "Executing in %s" % os.getcwd() )
+ for line in execute(cmd.split()):
+ send_msg(line, conn)
+ os.chdir(oldCWD)
+
+def find_files_to_run( files ):
+ """Any file name starting with __main is to be run."""
+ toRun = []
+ for f in files:
+ if '__main' in os.path.basename(f):
+ toRun.append(f)
+ if toRun:
+ return toRun
+
+ # Then guess.
+ if len(files) == 1:
+ return files
+
+ for f in files:
+ with open(f, 'r' ) as fh:
+ txt = fh.read()
+ if re.search(r'def\s+main\(', txt):
+ if re.search('^\s+main\(\S+?\)', txt):
+ toRun.append(f)
+ return toRun
+
+def recv_input(conn, size=1024):
+ # first 10 bytes always tell how much to read next. Make sure the submit job
+ # script has it
+ d = conn.recv(10, socket.MSG_WAITALL)
+ while len(d) < 10:
+ try:
+ d = conn.recv(10, socket.MSG_WAITALL)
+ except Exception:
+ _logger.error( "Error in format. First 6 bytes are size of msg." )
+ continue
+ d, data = int(d), b''
+ while len(data) < d:
+ data += conn.recv(d-len(data), socket.MSG_WAITALL)
+ return data
+
+def writeTarfile( data ):
+ tfile = os.path.join(tempfile.mkdtemp(), 'data.tar.bz2')
+ with open(tfile, 'wb' ) as f:
+ _logger.info( "Writing %d bytes to %s" % (len(data), tfile))
+ f.write(data)
+ # Sleep for some time so that file can be written to disk.
+ time.sleep(0.2)
+ if not tarfile.is_tarfile(tfile):
+ _logger.warn( 'Not a valid tar file: %s' % tfile)
+ return None
+ return tfile
+
+def suffixMatplotlibStmt( filename ):
+ outfile = '%s.1.py' % filename
+ with open(filename, 'r') as f:
+ txt = f.read()
+
+ matplotlibText = '''
+# from matplotlib.backends.backend_pdf import PdfPages
+import matplotlib.pyplot as plt
+
+def multipage(filename, figs=None, dpi=200):
+ pp = PdfPages(filename)
+ if figs is None:
+ figs = [plt.figure(n) for n in plt.get_fignums()]
+ for fig in figs:
+ fig.savefig(pp, format='pdf')
+ pp.close()
+
+def saveall(prefix='results', figs=None):
+ if figs is None:
+ figs = [plt.figure(n) for n in plt.get_fignums()]
+ for i, fig in enumerate(figs):
+ fig.savefig('%s.%d.png' %(prefix,i) )
+ plt.close()
+
+try:
+ # multipage("results.pdf")
+ saveall()
+except Exception as e:
+ print( e )
+ '''
+ with open(outfile, 'w' ) as f:
+ f.write( txt )
+ f.write( matplotlibText )
+ return outfile
+
+def run_file(filename, conn, cwd=None):
+ filename = suffixMatplotlibStmt(filename)
+ run( "%s %s" % (sys.executable, filename), conn, cwd)
+ _logger.info( '.... DONE' )
+
+def extract_files(tfile, to):
+ userFiles = []
+ with tarfile.open(tfile, 'r' ) as f:
+ userFiles = f.getnames( )
+ try:
+ f.extractall( to )
+ except Exception as e:
+ _logger.warn( e)
+ # now check if all files have been extracted properly
+ success = True
+ for f in userFiles:
+ if not os.path.exists(f):
+ _logger.error( "File %s could not be extracted." % f )
+ success = False
+ return userFiles
+
+def prepareMatplotlib( cwd ):
+ with open(os.path.join(cwd, 'matplotlibrc'), 'w') as f:
+ f.write( 'interactive : True' )
+
+def send_bz2(conn, data):
+ data = b'%010d%s' % (len(data), data)
+ conn.sendall(data)
+
+def sendResults(tdir, conn, fromThisTime):
+ # Only send new files.
+ resdir = tempfile.mkdtemp()
+ resfile = os.path.join(resdir, 'results.tar.bz2')
+
+ with tarfile.open( resfile, 'w|bz2') as tf:
+ for d, sd, fs in os.walk(tdir):
+ for f in fs:
+ fpath = os.path.join(d,f)
+ if datetime.datetime.fromtimestamp(os.path.getmtime(fpath)) > fromThisTime:
+ _logger.info( "Adding file %s" % f )
+ tf.add(os.path.join(d, f), f)
+
+ time.sleep(0.01)
+ # now send the tar file back to client
+ with open(resfile, 'rb' ) as f:
+ data = f.read()
+ _logger.info( 'Total bytes in result: %d' % len(data))
+ send_bz2(conn, data)
+ shutil.rmtree(resdir)
+
+def simulate( tfile, conn ):
+ """Simulate a given tar file.
+ """
+ tdir = os.path.dirname( tfile )
+ os.chdir( tdir )
+ userFiles = extract_files(tfile, tdir)
+ # Now simulate.
+ toRun = find_files_to_run(userFiles)
+ if len(toRun) < 1:
+ return 1
+ prepareMatplotlib(tdir)
+ status, msg = 0, ''
+ for _file in toRun:
+ try:
+ run_file(_file, conn, tdir)
+ except Exception as e:
+ msg += str(e)
+ status = 1
+ return status, msg
+
+def savePayload( conn ):
+ data = recv_input(conn)
+ tarfileName = writeTarfile(data)
+ return tarfileName, len(data)
+
+def handle_client(conn, ip, port):
+ isActive = True
+ while isActive:
+ tarfileName, nBytes = savePayload(conn)
+ if tarfileName is None:
+ _logger.warn( "Could not recieve data." )
+ isActive = False
+ _logger.info( "PAYLOAD RECIEVED: %d" % nBytes )
+ if not os.path.isfile(tarfileName):
+ send_msg("[ERROR] %s is not a valid tarfile. Retry"%tarfileName, conn)
+ break
+ startSimTime = datetime.datetime.now()
+ res, msg = simulate( tarfileName, conn )
+ if not res:
+ send_msg( "Failed to run simulation: %s" % msg, conn)
+ isActive = False
+ time.sleep(0.1)
+ send_msg('>DONE SIMULATION', conn)
+ # Send results after DONE is sent.
+ sendResults(os.path.dirname(tarfileName), conn, startSimTime)
+
+def start_server( host, port, max_requests = 10 ):
+ global stop_all_
+ soc = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+ soc.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
+ try:
+ soc.bind( (host, port))
+ _logger.info( "Server created %s:%s" %(host,port) )
+ except Exception as e:
+ _logger.error( "Failed to bind: %s" % e)
+ quit(1)
+
+ # listen upto 100 of requests
+ soc.listen(max_requests)
+ while True:
+ conn, (ip, port) = soc.accept()
+ _logger.info( "Connected with %s:%s" % (ip, port) )
+ try:
+ t = threading.Thread(target=handle_client, args=(conn, ip, port))
+ t.start()
+ except Exception as e:
+ _logger.warn(e)
+ if stop_all_:
+ break
+ soc.close()
+
+def serve(host, port):
+ start_server(host, port)
+
+def main( args ):
+ global stop_all_
+ host, port = args.host, args.port
+ try:
+ serve(host, port)
+ except KeyboardInterrupt:
+ stop_all_ = True
+ quit(1)
+
+if __name__ == '__main__':
+ import argparse
+ # Argument parser.
+ description = '''Run MOOSE server.'''
+ parser = argparse.ArgumentParser(description=description, add_help=False)
+ parser.add_argument( '--help', action='help', help='Show this msg and exit')
+ parser.add_argument('--host', '-h'
+ , required = False, default = socket.gethostbyname(socket.gethostname())
+ , help = 'Server Name'
+ )
+ parser.add_argument('--port', '-p'
+ , required = False, default = 31417, type=int
+ , help = 'Port number'
+ )
+ class Args: pass
+ args = Args()
+ parser.parse_args(namespace=args)
+ try:
+ main(args)
+ except KeyboardInterrupt as e:
+ stop_all_ = True
+ quit(1)
diff --git a/moose-core/python/rdesigneur/rdesigneur.py b/moose-core/python/rdesigneur/rdesigneur.py
index 6ad93d02b89981d95b1bc215df7d6e8ecffce079..c1cb25ec96a07353787257765479a6bfa90d1966 100644
--- a/moose-core/python/rdesigneur/rdesigneur.py
+++ b/moose-core/python/rdesigneur/rdesigneur.py
@@ -1249,7 +1249,6 @@ rdesigneur.rmoogli.updateMoogliViewer()
comptList[0].name = 'dend'
return comptList
if not self._isModelFromKkit():
- print( "Not isModelfromKkit" )
return comptList
sortedComptList = sorted( comptList, key=lambda x: -x.volume )
if self.addSomaChemCompt:
@@ -1393,7 +1392,11 @@ rdesigneur.rmoogli.updateMoogliViewer()
def _loadChem( self, fname, chemName ):
chem = moose.Neutral( '/library/' + chemName )
- modelId = moose.loadModel( fname, chem.path, 'ee' )
+ pre, ext = os.path.splitext( fname )
+ if ext == '.xml' or ext == '.sbml':
+ modelId = moose.mooseReadSBML( fname, chem.path )
+ else:
+ modelId = moose.loadModel( fname, chem.path, 'ee' )
comptlist = moose.wildcardFind( chem.path + '/#[ISA=ChemCompt]' )
if len( comptlist ) == 0:
print("loadChem: No compartment found in file: ", fname)
diff --git a/moose-core/python/rdesigneur/rdesigneurProtos.py b/moose-core/python/rdesigneur/rdesigneurProtos.py
index cade79201b388014a2719c513526a0c0eda63417..991bf4e8f313938571fa0dcf311c87f61aecda4b 100644
--- a/moose-core/python/rdesigneur/rdesigneurProtos.py
+++ b/moose-core/python/rdesigneur/rdesigneurProtos.py
@@ -239,7 +239,7 @@ def make_Ca( name ):
if ( x > EREST_ACT):
yA[i] = 5.0 * math.exp( -50 * (x - EREST_ACT) )
else:
- yA[i] = 0.0
+ yA[i] = 5.0
#yB[i] = 6.0 - yA[i]
yB[i] = 5.0
x += dx
@@ -336,6 +336,7 @@ def make_K_AHP( name ):
K_AHP.Xpower = 0
K_AHP.Ypower = 0
K_AHP.Zpower = 1
+ K_AHP.useConcentration = 1
zgate = moose.element( K_AHP.path + '/gateZ' )
xmax = 0.02 # 20 micromolar.
@@ -348,7 +349,7 @@ def make_K_AHP( name ):
x = zgate.min
for i in range( zgate.divs + 1 ):
zA[i] = min( 250.00 * CA_SCALE * x, 10 )
- zB[i] = 1.0
+ zB[i] = 1.0 + zA[i]
x = x + dx
zgate.tableA = zA
diff --git a/moose-core/scheduling/Clock.cpp b/moose-core/scheduling/Clock.cpp
index aad5c0666fa608e09e53c7ce1de7e4b69a297354..dd60aecf359bf4fc8698a40031a1f0fb2f6fc4a8 100644
--- a/moose-core/scheduling/Clock.cpp
+++ b/moose-core/scheduling/Clock.cpp
@@ -166,7 +166,8 @@ const Cinfo* Clock::initCinfo()
);
static ReadOnlyValueFinfo< Clock, unsigned int > stride(
"stride",
- "Number by which the simulation advances the current step on each cycle. stride = smallest active timestep/smallest defined timestep.",
+ "Number by which the simulation advances the current step on each cycle. "
+ "stride = smallest active timestep/smallest defined timestep.",
&Clock::getStride
);
static ReadOnlyValueFinfo< Clock, unsigned long > currentStep(
@@ -221,90 +222,90 @@ const Cinfo* Clock::initCinfo()
///////////////////////////////////////////////////////
// MsgDest definitions
///////////////////////////////////////////////////////
- static DestFinfo start( "start",
- "Sets off the simulation for the specified duration",
- new EpFunc2< Clock, double, bool >(&Clock::handleStart )
- );
-
- static DestFinfo step( "step",
- "Sets off the simulation for the specified # of steps. "
- "Here each step advances the simulation by the timestep of the "
- "smallest tick that is actually in use. ",
- new EpFunc1< Clock, unsigned long >(&Clock::handleStep )
- );
-
- static DestFinfo stop( "stop",
- "Halts the simulation, with option to restart seamlessly",
- new OpFunc0< Clock >(&Clock::stop )
- );
-
- static DestFinfo reinit( "reinit",
- "Zeroes out all ticks, starts at t = 0",
- new EpFunc0< Clock >(&Clock::handleReinit )
- );
+ static DestFinfo start( "start"
+ , "Sets off the simulation for the specified duration",
+ new EpFunc2< Clock, double, bool >(&Clock::handleStart )
+ );
+
+ static DestFinfo step( "step"
+ , "Sets off the simulation for the specified # of steps. "
+ "Here each step advances the simulation by the timestep of the "
+ "smallest tick that is actually in use. "
+ , new EpFunc1< Clock, unsigned long >(&Clock::handleStep )
+ );
+
+ static DestFinfo stop( "stop"
+ , "Halts the simulation, with option to restart seamlessly"
+ , new OpFunc0< Clock >(&Clock::stop )
+ );
+
+ static DestFinfo reinit( "reinit"
+ , "Zeroes out all ticks, starts at t = 0"
+ , new EpFunc0< Clock >(&Clock::handleReinit )
+ );
static Finfo* clockControlFinfos[] =
{
&start, &step, &stop, &reinit,
};
+
///////////////////////////////////////////////////////
// SharedFinfo for Shell to control Clock
- ///////////////////////////////////////////////////////
- static SharedFinfo clockControl( "clockControl",
- "Controls all scheduling aspects of Clock, usually from Shell",
- clockControlFinfos,
- sizeof( clockControlFinfos ) / sizeof( Finfo* )
- );
+ static SharedFinfo clockControl( "clockControl"
+ , "Controls all scheduling aspects of Clock, usually from Shell"
+ , clockControlFinfos
+ , sizeof( clockControlFinfos ) / sizeof( Finfo* )
+ );
static Finfo* clockFinfos[] =
{
// Fields
- &dt, // Value
- &runTime, // ReadOnlyValue
- ¤tTime, // ReadOnlyValue
- &nsteps, // ReadOnlyValue
- &numTicks, // ReadOnlyValue
- &stride, // ReadOnlyValue
- ¤tStep, // ReadOnlyValue
- &dts, // ReadOnlyValue
- &isRunning, // ReadOnlyValue
- &tickStep, // LookupValue
- &tickDt, // LookupValue
- &defaultTick, // ReadOnlyLookupValue
- &clockControl, // Shared
- finished(), // Src
- procs[0], // Src
- procs[1], // Src
- procs[2], // Src
- procs[3], // Src
- procs[4], // Src
- procs[5], // Src
- procs[6], // Src
- procs[7], // Src
- procs[8], // Src
- procs[9], // Src
- procs[10], // Src
- procs[11], // Src
- procs[12], // Src
- procs[13], // Src
- procs[14], // Src
- procs[15], // Src
- procs[16], // Src
- procs[17], // Src
- procs[18], // Src
- procs[19], // Src
- procs[20], // Src
- procs[21], // Src
- procs[22], // Src
- procs[23], // Src
- procs[24], // Src
- procs[25], // Src
- procs[26], // Src
- procs[27], // Src
- procs[28], // Src
- procs[29], // Src
- procs[30], // Src
- procs[31], // Src
+ &dt, // Value
+ &runTime, // ReadOnlyValue
+ ¤tTime, // ReadOnlyValue
+ &nsteps, // ReadOnlyValue
+ &numTicks, // ReadOnlyValue
+ &stride, // ReadOnlyValue
+ ¤tStep, // ReadOnlyValue
+ &dts, // ReadOnlyValue
+ &isRunning, // ReadOnlyValue
+ &tickStep, // LookupValue
+ &tickDt, // LookupValue
+ &defaultTick, // ReadOnlyLookupValue
+ &clockControl, // Shared
+ finished(), // Src
+ procs[0], // Src
+ procs[1], // Src
+ procs[2], // Src
+ procs[3], // Src
+ procs[4], // Src
+ procs[5], // Src
+ procs[6], // Src
+ procs[7], // Src
+ procs[8], // Src
+ procs[9], // Src
+ procs[10], // Src
+ procs[11], // Src
+ procs[12], // Src
+ procs[13], // Src
+ procs[14], // Src
+ procs[15], // Src
+ procs[16], // Src
+ procs[17], // Src
+ procs[18], // Src
+ procs[19], // Src
+ procs[20], // Src
+ procs[21], // Src
+ procs[22], // Src
+ procs[23], // Src
+ procs[24], // Src
+ procs[25], // Src
+ procs[26], // Src
+ procs[27], // Src
+ procs[28], // Src
+ procs[29], // Src
+ procs[30], // Src
+ procs[31], // Src
};
static string doc[] =
@@ -348,89 +349,90 @@ const Cinfo* Clock::initCinfo()
"different time-resolutions. Typically one uses tick 8 and 18.\n"
"Here are the detailed mappings of class to tick.\n"
" Class Tick dt \n"
- " DiffAmp 0 50e-6\n"
- " Interpol 0 50e-6\n"
- " PIDController 0 50e-6\n"
- " PulseGen 0 50e-6\n"
- " StimulusTable 0 50e-6\n"
- " testSched 0 50e-6\n"
- " VClamp 0 50e-6\n"
- " SynHandlerBase 1 50e-6\n"
- " SimpleSynHandler 1 50e-6\n"
- " STDPSynHandler 1 50e-6\n"
+ " DiffAmp 0 50e-6\n"
+ " Interpol 0 50e-6\n"
+ " PIDController 0 50e-6\n"
+ " PulseGen 0 50e-6\n"
+ " StimulusTable 0 50e-6\n"
+ " testSched 0 50e-6\n"
+ " VClamp 0 50e-6\n"
+ " SynHandlerBase 1 50e-6\n"
+ " SimpleSynHandler 1 50e-6\n"
+ " STDPSynHandler 1 50e-6\n"
" GraupnerBrunel2012CaPlasticitySynHandler 1 50e-6\n"
- " SeqSynHandler 1 50e-6\n"
- " CaConc 1 50e-6\n"
- " CaConcBase 1 50e-6\n"
- " DifShell 1 50e-6\n"
- " DifShellBase 1 50e-6\n"
- " MMPump 1 50e-6\n"
- " DifBuffer 1 50e-6\n"
- " DifBufferBase 1 50e-6\n"
- " MgBlock 1 50e-6\n"
- " Nernst 1 50e-6\n"
- " RandSpike 1 50e-6\n"
- " ChanBase 2 50e-6\n"
- " IntFire 2 50e-6\n"
- " IntFireBase 2 50e-6\n"
- " LIF 2 50e-6\n"
- " QIF 2 50e-6\n"
- " ExIF 2 50e-6\n"
- " AdExIF 2 50e-6\n"
- " AdThreshIF 2 50e-6\n"
- " IzhIF 2 50e-6\n"
- " IzhikevichNrn 2 50e-6\n"
- " SynChan 2 50e-6\n"
- " NMDAChan 2 50e-6\n"
- " GapJunction 2 50e-6\n"
- " HHChannel 2 50e-6\n"
- " HHChannel2D 2 50e-6\n"
- " Leakage 2 50e-6\n"
- " MarkovChannel 2 50e-6\n"
- " MarkovGslSolver 2 50e-6\n"
- " MarkovRateTable 2 50e-6\n"
- " MarkovSolver 2 50e-6\n"
- " MarkovSolverBase 2 50e-6\n"
- " RC 2 50e-6\n"
- " Compartment (init) 3 50e-6\n"
- " CompartmentBase (init ) 3 50e-6\n"
- " SymCompartment (init) 3 50e-6\n"
- " Compartment 4 50e-6\n"
- " CompartmentBase 4 50e-6\n"
- " SymCompartment 4 50e-6\n"
- " SpikeGen 5 50e-6\n"
- " HSolve 6 50e-6\n"
- " SpikeStats 7 50e-6\n"
- " Table 8 0.1e-3\n"
- " TimeTable 8 0.1e-3\n"
-
- " Dsolve 10 0.01\n"
- " Adaptor 11 0.1\n"
- " Func 12 0.1\n"
- " Function 12 0.1\n"
- " Arith 12 0.1\n"
- " BufPool 13 0.1\n"
- " Pool 13 0.1\n"
- " PoolBase 13 0.1\n"
- " CplxEnzBase 14 0.1\n"
- " Enz 14 0.1\n"
- " EnzBase 14 0.1\n"
- " MMenz 14 0.1\n"
- " Reac 14 0.1\n"
- " ReacBase 14 0.1\n"
- " Gsolve (init) 15 0.1\n"
- " Ksolve (init) 15 0.1\n"
- " Gsolve 16 0.1\n"
- " Ksolve 16 0.1\n"
- " Stats 17 0.1\n"
- " Table2 18 1\n"
- " Streamer 19 10\n"
-
- " HDF5DataWriter 30 1\n"
- " HDF5WriterBase 30 1\n"
- " NSDFWriter 30 1\n"
- " PyRun 30 1\n"
- " PostMaster 31 0.01\n"
+ " SeqSynHandler 1 50e-6\n"
+ " CaConc 1 50e-6\n"
+ " CaConcBase 1 50e-6\n"
+ " DifShell 1 50e-6\n"
+ " DifShellBase 1 50e-6\n"
+ " MMPump 1 50e-6\n"
+ " DifBuffer 1 50e-6\n"
+ " DifBufferBase 1 50e-6\n"
+ " MgBlock 1 50e-6\n"
+ " Nernst 1 50e-6\n"
+ " RandSpike 1 50e-6\n"
+ " ChanBase 2 50e-6\n"
+ " IntFire 2 50e-6\n"
+ " IntFireBase 2 50e-6\n"
+ " LIF 2 50e-6\n"
+ " QIF 2 50e-6\n"
+ " ExIF 2 50e-6\n"
+ " AdExIF 2 50e-6\n"
+ " AdThreshIF 2 50e-6\n"
+ " IzhIF 2 50e-6\n"
+ " IzhikevichNrn 2 50e-6\n"
+ " SynChan 2 50e-6\n"
+ " NMDAChan 2 50e-6\n"
+ " GapJunction 2 50e-6\n"
+ " HHChannel 2 50e-6\n"
+ " HHChannel2D 2 50e-6\n"
+ " Leakage 2 50e-6\n"
+ " MarkovChannel 2 50e-6\n"
+ " MarkovGslSolver 2 50e-6\n"
+ " MarkovRateTable 2 50e-6\n"
+ " MarkovSolver 2 50e-6\n"
+ " MarkovSolverBase 2 50e-6\n"
+ " RC 2 50e-6\n"
+ " Compartment (init) 3 50e-6\n"
+ " CompartmentBase (init ) 3 50e-6\n"
+ " SymCompartment (init) 3 50e-6\n"
+ " Compartment 4 50e-6\n"
+ " CompartmentBase 4 50e-6\n"
+ " SymCompartment 4 50e-6\n"
+ " SpikeGen 5 50e-6\n"
+ " HSolve 6 50e-6\n"
+ " SpikeStats 7 50e-6\n"
+ " Table 8 0.1e-3\n"
+ " TimeTable 8 0.1e-3\n"
+
+ " Dsolve 10 0.01\n"
+ " Adaptor 11 0.1\n"
+ " Func 12 0.1\n"
+ " Function 12 0.1\n"
+ " Arith 12 0.1\n"
+ " BufPool 13 0.1\n"
+ " Pool 13 0.1\n"
+ " PoolBase 13 0.1\n"
+ " CplxEnzBase 14 0.1\n"
+ " Enz 14 0.1\n"
+ " EnzBase 14 0.1\n"
+ " MMenz 14 0.1\n"
+ " Reac 14 0.1\n"
+ " ReacBase 14 0.1\n"
+ " Gsolve (init) 15 0.1\n"
+ " Ksolve (init) 15 0.1\n"
+ " Gsolve 16 0.1\n"
+ " Ksolve 16 0.1\n"
+ " Stats 17 0.1\n"
+ " Table2 18 1\n"
+ " SocketStreamer 19 5\n"
+ " Streamer 20 10\n"
+
+ " HDF5DataWriter 30 1\n"
+ " HDF5WriterBase 30 1\n"
+ " NSDFWriter 30 1\n"
+ " PyRun 30 1\n"
+ " PostMaster 31 0.01\n"
" \n"
" Note that the other classes are not scheduled at all.",
};
@@ -748,22 +750,22 @@ void Clock::handleStep( const Eref& e, unsigned long numSteps )
for( unsigned int i = 0; i < numThreads_; ++i )
{
std::async( std::launch::async
- , [this,blockSize,i,nTasks,endStep,e]
+ , [this,blockSize,i,nTasks,endStep,e]
+ {
+ unsigned int mapI = i * blockSize;
+ // Get the block we want to run in paralle.
+ for( unsigned int ii = i * blockSize; ii < min((i+1) * blockSize, nTasks); ii++ )
{
- unsigned int mapI = i * blockSize;
- // Get the block we want to run in paralle.
- for( unsigned int ii = i * blockSize; ii < min((i+1) * blockSize, nTasks); ii++ )
+ unsigned int j = activeTicks_[ ii ];
+ if( endStep % j == 0 )
{
- unsigned int j = activeTicks_[ ii ];
- if( endStep % j == 0 )
- {
- info_.dt = j * dt_;
- processVec( )[ activeTicksMap_[mapI] ]->send( e, &info_ );
- }
- mapI++;
+ info_.dt = j * dt_;
+ processVec( )[ activeTicksMap_[mapI] ]->send( e, &info_ );
}
+ mapI++;
}
- );
+ }
+ );
}
#else
vector< unsigned int >::const_iterator k = activeTicksMap_.begin();
@@ -783,13 +785,13 @@ void Clock::handleStep( const Eref& e, unsigned long numSteps )
// true.
if( notify_ )
{
- if( fmod(100 * currentTime_ / runTime_ , 10.0) == 0.0 )
+ if( fmod(100 * currentTime_ / runTime_, 10.0) == 0.0 )
{
time( &rawtime );
timeinfo = localtime( &rawtime );
strftime(now, 80, "%c", timeinfo);
cout << "@ " << now << ": " << 100 * currentTime_ / runTime_
- << "% of total " << runTime_ << " seconds is over." << endl;
+ << "% of total " << runTime_ << " seconds is over." << endl;
}
}
@@ -826,6 +828,7 @@ void Clock::handleReinit( const Eref& e )
info_.dt = *j * dt_;
reinitVec()[*k++]->send( e, &info_ );
}
+
info_.dt = dt_;
doingReinit_ = false;
}
@@ -946,7 +949,10 @@ void Clock::buildDefaultTick()
defaultTick_["Stats"] = 17;
defaultTick_["Table2"] = 18;
- defaultTick_["Streamer"] = 19;
+
+ defaultTick_["SocketStreamer"] = 19;
+ defaultTick_["Streamer"] = 20;
+
defaultTick_["HDF5DataWriter"] = 30;
defaultTick_["HDF5WriterBase"] = 30;
defaultTick_["NSDFWriter"] = 30;
@@ -1013,9 +1019,9 @@ 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;
@@ -1023,8 +1029,9 @@ void Clock::buildDefaultTick()
defaultDt_[15] = 0.1;
defaultDt_[16] = 0.1;
defaultDt_[17] = 0.1;
- defaultDt_[18] = 1; // For tables for chemical calculations.
- defaultDt_[19] = 10; // For Streamer
+ defaultDt_[18] = 1; // For tables for chemical calculations.
+ defaultDt_[19] = 5; // For Socket Streamer
+ defaultDt_[20] = 10; // For CSV Streamer
// 20-29 are not assigned.
defaultDt_[30] = 1; // For the HDF writer
diff --git a/moose-core/scripts/Makefile.wheel b/moose-core/scripts/Makefile.wheel
deleted file mode 100644
index 86f502625bb50ba083a52562f3e39395e2d9fc83..0000000000000000000000000000000000000000
--- a/moose-core/scripts/Makefile.wheel
+++ /dev/null
@@ -1,18 +0,0 @@
-all : fix
- @echo "All done"
-
-wheel : ./setup.wheel.py
- python ./setup.wheel.py bdist_wheel
-
-check : wheel
- auditwheel show dist/*.whl
- echo "If successful then run `make fix`"
-
-fix : check
- auditwheel repair dist/*.whl
-
-upload : fix
- twine upload dist/*.whl
-
-
-
diff --git a/moose-core/scripts/Portfile b/moose-core/scripts/Portfile
deleted file mode 100644
index ee48c5682dea494e165937a62404947029f42a5c..0000000000000000000000000000000000000000
--- a/moose-core/scripts/Portfile
+++ /dev/null
@@ -1,56 +0,0 @@
-# $Id$
-
-PortSystem 1.0
-
-name moose
-version 3.0.2
-categories science
-platforms darwin
-maintainers dilawars \
- ncbs.res.in:dilawars
-description MOOSE is the Multiscale Object-Oriented Simulation \
- Environment.
-long_description MOOSE is the Multiscale Object-Oriented Simulation \
- Environment.
-
-homepage http://moose.ncbs.res.in
-fetch.type git
-fetch.ignore_sslcert yes
-git.url https://github.com/BhallaLab/moose-core
-git.branch master
-license GPL-3
-
-
-depends_build port:cmake \
- port:python27 \
- port:gsl \
- port:hdf5 \
-
-depends_lib port:gsl \
- port:hdf5 \
- port:py27-matplotlib \
- port:py27-numpy \
- port:python27 \
-
-set python_branch 2.7
-
-configure.cmd {
- mkdir -p _build
- cd _build
- cmake -DCMAKE_INSTALL_PREFIX=${prefix} ..
-}
-configure.args VERBOSE=1
-configure.pre_args ""
-configure.post_args ""
-
-build.cmd cd _build && make
-build.pre_args ""
-build.post_args ""
-
-test.cmd cd _build && ctest --output-on-failure
-
-##destroot.cmd cd _build && make install DESTDIR=${destdir}
-##destroot.args ""
-##destroot.pre_args ""
-##destroot.post_args ""
-##destroot.destdir prefix=${destroot}/${prefix}
diff --git a/moose-core/scripts/build-moose-core b/moose-core/scripts/build-moose-core
deleted file mode 100755
index 61d0abacb1feff866cd2bbd50bd0691cf732fba3..0000000000000000000000000000000000000000
--- a/moose-core/scripts/build-moose-core
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/sh
-
-#if one needs SBML support pass USE_SBML=1 else pass USE_SBML=0,
-#if USE_SBML=1 is used make sure libSBML is installed and "libSBML-5.9.0" is currently supported
-
-(make clean; make USE_SBML=1)
-local_site_package_directory=`python -c "import site; print site.getusersitepackages()"`
-mkdir -p "$local_site_package_directory"
-echo $(echo `pwd` | sed "s/\/[^\/]*$//")'/moose-core/python' > "$local_site_package_directory/moose.pth"
-#echo "`pwd`/moose-core/python" > "$local_site_package_directory/moose.pth"
-
diff --git a/moose-core/scripts/build_debian.sh b/moose-core/scripts/build_debian.sh
deleted file mode 100755
index f0f9247ee5b9c87b133c7cfda5476024da390872..0000000000000000000000000000000000000000
--- a/moose-core/scripts/build_debian.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env bash
-# This script is for launchpad.
-(
-set -e
-set -o xtrace
-cd ..
-cat > moose.recipe <<EOF
-# bzr-builder format 0.3 deb-version {debupstream}+{revno}
-lp:moose
-EOF
-# one can do nesting here.
-if [ $# -gt 0 ]; then
- if [[ "$1" == "update" ]]; then
- echo "Fetching repo and creating tar-ball"
- bzr dailydeb --allow-fallback-to-native moose.recipe ..
- elif [[ "$1" == "pbuilder" ]]; then
- bzr dailydeb --allow-fallback-to-native moose.recipe ..
- sudo -E pbuilder build ../*.dsc
- exit
- fi
-fi
-
-tarFile=`find .. -type f -maxdepth 1 -name "moose_3.0*.tar.gz"`
-echo "Found tarfiles are $tarFile"
-if [[ ! $tarFile ]]; then
- echo "I could not file a tar.gz file. Can't continue"
- echo "++ Cleaning previous mess"
- rm -rf ../moose_3.0* ../moose-{*
- echo "++ Let me download a fresh one"
- bzr dailydeb --allow-fallback-to-native moose.recipe ..
-fi
-
-rm -f moose.recipe
-echo "Building debian package"
-bzr builddeb -- -uc -us
-)
diff --git a/moose-core/scripts/build_debian_locally_on_ubuntu.sh b/moose-core/scripts/build_debian_locally_on_ubuntu.sh
deleted file mode 100755
index a7ba62b2e557d76e094edb78bc73c1ab3bb3ea18..0000000000000000000000000000000000000000
--- a/moose-core/scripts/build_debian_locally_on_ubuntu.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/env bash
-(
- cd ..
- debuild -uc -us
-)
diff --git a/moose-core/scripts/build_debian_using_bzr.sh b/moose-core/scripts/build_debian_using_bzr.sh
deleted file mode 100755
index f0f9247ee5b9c87b133c7cfda5476024da390872..0000000000000000000000000000000000000000
--- a/moose-core/scripts/build_debian_using_bzr.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env bash
-# This script is for launchpad.
-(
-set -e
-set -o xtrace
-cd ..
-cat > moose.recipe <<EOF
-# bzr-builder format 0.3 deb-version {debupstream}+{revno}
-lp:moose
-EOF
-# one can do nesting here.
-if [ $# -gt 0 ]; then
- if [[ "$1" == "update" ]]; then
- echo "Fetching repo and creating tar-ball"
- bzr dailydeb --allow-fallback-to-native moose.recipe ..
- elif [[ "$1" == "pbuilder" ]]; then
- bzr dailydeb --allow-fallback-to-native moose.recipe ..
- sudo -E pbuilder build ../*.dsc
- exit
- fi
-fi
-
-tarFile=`find .. -type f -maxdepth 1 -name "moose_3.0*.tar.gz"`
-echo "Found tarfiles are $tarFile"
-if [[ ! $tarFile ]]; then
- echo "I could not file a tar.gz file. Can't continue"
- echo "++ Cleaning previous mess"
- rm -rf ../moose_3.0* ../moose-{*
- echo "++ Let me download a fresh one"
- bzr dailydeb --allow-fallback-to-native moose.recipe ..
-fi
-
-rm -f moose.recipe
-echo "Building debian package"
-bzr builddeb -- -uc -us
-)
diff --git a/moose-core/scripts/build_macosx_bundle.sh b/moose-core/scripts/build_macosx_bundle.sh
deleted file mode 100755
index cd5fbb6175aad1df30e818e1d61b5c6ba3dbbedf..0000000000000000000000000000000000000000
--- a/moose-core/scripts/build_macosx_bundle.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/bash
-mkdir -p _build
-(
- cd _build
- rm -f moose*.dmg
- rm -rf moose-3.0.1-Linux*
- cmake -DCMAKE_INSTALL_PREFIX=/Moose.app ..
- make -j4
- #cpack -G Bundle
- cpack -G DragNDrop -V
- 7z x moose-3.0.1-Linux-.dmg
-)
diff --git a/moose-core/scripts/build_pypi.sh b/moose-core/scripts/build_pypi.sh
deleted file mode 100755
index 486bd2421174415fa08c46c5d920a03309a02e58..0000000000000000000000000000000000000000
--- a/moose-core/scripts/build_pypi.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/bin/bash
-set -e
-# This creates a package for pip. For testing purpose
-moose_dir=moose-3.0
-(
- cd ..
- svn export --force . scripts/$moose_dir
-)
-(
- cp setup.py $moose_dir/
- cd $moose_dir
- echo "Creating new archive"
- if [ -f dist/$moose_dir.tar.gz ]; then
- rm -f dist/*.tar.gz
- fi
- python setup.py sdist -vv
- echo "Created new archive"
- sudo pip install dist/*.tar.gz --no-clean
- echo "Do the rest in $moose_dir"
-)
diff --git a/moose-core/scripts/build_using_gcc_on_mac.sh b/moose-core/scripts/build_using_gcc_on_mac.sh
deleted file mode 100755
index d3b13406f710065085156118dd48fc78a7fa7d43..0000000000000000000000000000000000000000
--- a/moose-core/scripts/build_using_gcc_on_mac.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-mkdir -p _build
-(
- cd _build
- cmake -DCMAKE_C_COMPILER=gcc-mp-4.8 \
- -DCMAKE_CXX_COMPILER=g++-mp-4.8 .. \
- -DCMAKE_CXX_LINK_EXECUTABLE=/opt/local/bin/ld
- make VERBOSE=1 -j4
-)
diff --git a/moose-core/scripts/cmake_sanity_check.py b/moose-core/scripts/cmake_sanity_check.py
deleted file mode 100755
index 075eb8b6b4a8aa2fe55771cafd5c181e162b0671..0000000000000000000000000000000000000000
--- a/moose-core/scripts/cmake_sanity_check.py
+++ /dev/null
@@ -1,98 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-"""cmake_sanity_check.py: Check if Cmake files are ok.
-
-Last modified: Sat Jan 18, 2014 05:01PM
-
-NOTE: Run in this directory only.
-
-"""
-
-__author__ = "Dilawar Singh"
-__copyright__ = "Copyright 2013, Dilawar Singh and NCBS Bangalore"
-__credits__ = ["NCBS Bangalore"]
-__license__ = "GNU GPL"
-__version__ = "1.0.0"
-__maintainer__ = "Dilawar Singh"
-__email__ = "dilawars@ncbs.res.in"
-__status__ = "Development"
-
-import sys
-import os
-import re
-from collections import defaultdict
-
-makefiles = {}
-cmakefiles = {}
-makedirs = set()
-cmakedirs = set()
-
-def check(d):
- searchMakefiles(d)
- checkMissingCMake()
- checkSrcs()
-
-def checkMissingCMake():
- if (makedirs - cmakedirs):
- print("[Failed] Test 1")
- print("Following directories have Makefile but not a CMakeFiles.txt file.")
- print("%s" % "\t\n".join(makedirs - cmakedirs))
-
-def searchMakefiles(topdir):
- for d, subd, fs in os.walk(topdir):
- if "../_build" in d or ".." == d: continue
- if "CMakeLists.txt" in fs:
- cmakedirs.add(d)
- cmakefiles[d] = fs
- if "Makefile" in fs:
- if "_build" in d:
- continue
- else:
- makedirs.add(d)
- makefiles[d] = fs
- else: pass
-
-def checkSrcs():
- objPat = re.compile(r"\w+\.o")
- srcPat = re.compile(r"\w+\.cpp")
- srcs = []
- csrcs = []
- for d in makefiles:
- with open(os.path.join(d, "Makefile"), "r") as f:
- txt = f.read()
- for i in txt.split("\n\n"):
- if "OBJ =" in i.upper():
- for j in i.split():
- if ".o" in j.strip():
- srcs.append("%s"%(j.strip()))
- try:
- with open(os.path.join(d, "CMakeLists.txt"), "r") as f:
- txt = f.read()
- csrcs = srcPat.findall(txt)
- except:
- print("Dir {} does not have CMakeLists.txt".format(d))
- csrcs = []
- #print("[TEST 2] Checking if CMake is creating extra objects")
- for csr in csrcs:
- objName = csr.replace(".cpp", ".o")
- if objName in srcs:
- pass
- else:
- print(" Failed: In dir {}, CMake is creating extra object {}".format(d, objName))
-
- pass
- print("[TEST 3] Checking if CMake is missing some objects")
- for obj in srcs:
- srcName = obj.replace(".o", ".cpp")
- if srcName in csrcs: pass
- else:
- print(" Failed: In dir {}, CMake is missing object {}".format(d,
- srcName))
-
-def main():
- test_dir = sys.argv[1]
- check(test_dir)
-
-
-if __name__ == '__main__':
- main()
diff --git a/moose-core/scripts/color.sh b/moose-core/scripts/color.sh
deleted file mode 100755
index abac71107e7bc7f3793af150c98c8bdb93154fce..0000000000000000000000000000000000000000
--- a/moose-core/scripts/color.sh
+++ /dev/null
@@ -1,48 +0,0 @@
-# Definitions of colors in bash
-RESTORE='\033[0m'
-
-RED='\033[00;31m'
-GREEN='\033[00;32m'
-YELLOW='\033[00;33m'
-BLUE='\033[00;34m'
-PURPLE='\033[00;35m'
-CYAN='\033[00;36m'
-LIGHTGRAY='\033[00;37m'
-
-LRED='\033[01;31m'
-LGREEN='\033[01;32m'
-LYELLOW='\033[01;33m'
-LBLUE='\033[01;34m'
-LPURPLE='\033[01;35m'
-LCYAN='\033[01;36m'
-WHITE='\033[01;37m'
-
-function colorPrint
-{
- case $1 in
- "WARN")
- echo -e "[WARN] ${LRED} $2 ${RESTORE} $3"
- ;;
- "INFO")
- echo -e "[INFO] ${LGREEN} $2 ${RESTORE} $3"
- ;;
- "ERROR")
- echo -e "[ERROR] ${RED} $2 ${RESTORE} $3"
- ;;
- "DEBUG")
- echo -e "[DEBUG] ${YELLOW} $2 ${RESTORE} $3"
- ;;
- "STEP")
- echo -e "[STEP] ${BLUE} $2 ${RESTORE} $3"
- ;;
- "TODO")
- echo -e "[TODO] ${CYAN} $2 ${RESTORE} $3"
- ;;
- "||")
- echo -e "|| ${PURPLE} $2 ${RESTORE} $3"
- ;;
- *)
- echo -e "[$1] $2 $3"
- ;;
- esac
-}
diff --git a/moose-core/scripts/moose b/moose-core/scripts/moose
deleted file mode 100755
index 97ae8a36b4402246c529d0b770367165ca4c6d78..0000000000000000000000000000000000000000
--- a/moose-core/scripts/moose
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-moose.bin "$@"
diff --git a/moose-core/scripts/moose.desktop b/moose-core/scripts/moose.desktop
deleted file mode 100644
index 2b95bd6e0ab88f2a18df6f2f1bae6a3e3f7f22a7..0000000000000000000000000000000000000000
--- a/moose-core/scripts/moose.desktop
+++ /dev/null
@@ -1,8 +0,0 @@
-[Desktop Entry]
-Name=MOOSE
-GenericName=MOOSE
-Exec=moosegui
-Type=Application
-Version=3.0
-Icon=/usr/share/icons/moose/moose.png
-Categories=Education;Science;Education;Chemistry;
diff --git a/moose-core/scripts/moosegui b/moose-core/scripts/moosegui
deleted file mode 100755
index 3acf2262e24990a7e3ffd8a496301b0ddf83e65a..0000000000000000000000000000000000000000
--- a/moose-core/scripts/moosegui
+++ /dev/null
@@ -1,3 +0,0 @@
-#/bin/bash
-# This script launches MOOSE gui.
-cd /usr/lib/moose/gui && python mgui.py
diff --git a/moose-core/scripts/moosegui.py b/moose-core/scripts/moosegui.py
deleted file mode 100755
index 40feef0c824f3cab0c2fdcae482baf030b6dccc0..0000000000000000000000000000000000000000
--- a/moose-core/scripts/moosegui.py
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# 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.
-
-import sys
-
-from mgui import mgui
-
-def main():
- mgui.main()
-
-if __name__ == '__main__':
- main()
-
diff --git a/moose-core/scripts/postinst b/moose-core/scripts/postinst
deleted file mode 100755
index 11fdb89b1850299f47dfc5c6a76d13b684e69f85..0000000000000000000000000000000000000000
--- a/moose-core/scripts/postinst
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/bin/sh
-# postinst script for moose
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postinst> `configure' <most-recently-configured-version>
-# * <old-postinst> `abort-upgrade' <new version>
-# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
-# <new-version>
-# * <postinst> `abort-remove'
-# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
-# <failed-install-package> <version> `removing'
-# <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- configure)
- cd /usr/lib/moose/python && python setup.py install --record installed_files.txt
- ;;
-
- abort-upgrade|abort-remove|abort-deconfigure)
- ;;
-
- *)
- echo "postinst called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/moose-core/scripts/prerm b/moose-core/scripts/prerm
deleted file mode 100755
index 3c976a65748cbd399ea44c3230bb7a313ea4e9f2..0000000000000000000000000000000000000000
--- a/moose-core/scripts/prerm
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/bin/sh
-# prerm script for moose
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <prerm> `remove'
-# * <old-prerm> `upgrade' <new-version>
-# * <new-prerm> `failed-upgrade' <old-version>
-# * <conflictor's-prerm> `remove' `in-favour' <package> <new-version>
-# * <deconfigured's-prerm> `deconfigure' `in-favour'
-# <package-being-installed> <version> `removing'
-# <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- remove|upgrade|deconfigure)
- if [ -d /usr/lib/moose/python ]; then
- ( cd /usr/lib/moose/python && cat installed_files.txt | xargs rm -rf )
- fi
-
- if [ -d /usr/lib/moose ]; then
- rm -R /usr/lib/moose
- fi
-
- if [ -d /usr/share/doc/moose ]; then
- rm -R /usr/share/doc/moose
- fi
-
- if [ -d /usr/share/moose ]; then
- rm -R /usr/share/moose
- fi
-
- if [ -d /usr/share/pyshared/moose ]; then
- rm -R /usr/share/pyshared/moose
- fi
-
- pydistpkg_dir=`python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())"`
- if [ -d $pydistpkg_dir/moose ];
- then
- rm -R $pydistpkg_dir/moose
- fi
- if [ -f $HOME/Desktop/MooseGUI.desktop ];
- then
- rm $HOME/Desktop/MooseGUI.desktop
- fi
- if [ -f $HOME/Desktop/HHSquidDemo.desktop ];
- then
- rm $HOME/Desktop/HHSquidDemo.desktop
- fi
-
- ;;
-
- failed-upgrade)
- ;;
-
- *)
- echo "prerm called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/moose-core/scripts/submit.py b/moose-core/scripts/submit.py
new file mode 100755
index 0000000000000000000000000000000000000000..931187361789959a7f6e31e5cc76bddd23d86414
--- /dev/null
+++ b/moose-core/scripts/submit.py
@@ -0,0 +1,147 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+from __future__ import division, print_function
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2017-, Dilawar Singh"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+import sys
+import os
+import socket
+import time
+import tarfile
+import tempfile
+
+def gen_prefix( msg, maxlength = 10 ):
+ msg = '>%s' % msg
+ if len(msg) < maxlength:
+ msg += ' ' * (maxlength - len(msg))
+ return msg[:maxlength].encode( 'utf-8' )
+
+def write_data_to_socket(conn, msg):
+ msg = b'%010d%s' % (len(msg), msg)
+ conn.sendall(msg)
+
+def relativePath(path, base):
+ return os.path.relpath(path, base)
+
+def gen_payload( args ):
+ path = args.path
+ archive = os.path.join(tempfile.mkdtemp(), 'data.tar.bz2')
+
+ # This mode (w|bz2) is suitable for streaming. The blocksize is default to
+ # 20*512 bytes. We change this to 2048
+ with tarfile.open(archive, 'w|bz2', bufsize=2048 ) as h:
+ if len(args.main) > 0:
+ for i, f in enumerate(args.main):
+ h.add(f, arcname='__main__%d.py'%i)
+ if os.path.isfile(path):
+ h.add(path, os.path.basename(path))
+ elif os.path.isdir(path):
+ for d, ds, fs in os.walk(path):
+ for f in fs:
+ p = os.path.join(d, f)
+ h.add(os.path.realpath(p), arcname=relativePath(p, path))
+ else:
+ print( "[ERROR] Neither file nor directory %s" % path )
+
+
+ with open(archive, 'rb') as f:
+ data = f.read()
+ return data
+
+def offload( args ):
+ zfile = create_zipfile( args.path )
+ send_zip( zfile )
+
+def loop( sock ):
+ sock.settimeout(1e-2)
+ while True:
+ try:
+ d = sock.recv(10).strip()
+ if len(d) > 0:
+ print(d)
+ except socket.timeout as e:
+ print( '.', end='' )
+ sys.stdout.flush()
+
+def read_msg(conn):
+ d = conn.recv(1024)
+ try:
+ d = d.decode('utf8').strip()
+ except Exception as e:
+ pass
+ return d
+
+def save_bz2(conn, outfile):
+ # first 6 bytes always tell how much to read next. Make sure the submit job
+ # script has it
+ d = conn.recv(10)
+ while len(d) < 10:
+ try:
+ d = conn.recv(10)
+ except Exception as e:
+ print( "[ERROR] Error in format. First 6 bytes are size of msg." )
+ continue
+
+ print( "Needs to get %s bytes" % d )
+ data = conn.recv(int(d))
+ with open(outfile, 'wb') as f:
+ f.write(data)
+ return data
+
+def main( args ):
+ sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+ try:
+ host, port = args.server.split(':')
+ sock.connect( (host, int(port)) )
+ sock.settimeout(1)
+ except Exception as e:
+ print( "[ERROR] Failed to connect to %s... " % args.server )
+ print( e )
+ quit()
+
+ data = gen_payload( args )
+ print( "[INFO ] Total bytes to send: %d" % len(data), end = '')
+ write_data_to_socket(sock, data)
+ print( ' ... [SENT]' )
+ while True:
+ try:
+ d = read_msg( sock )
+ print( d )
+ if '>DONE SIMULATION' in d:
+ break
+ except socket.timeout as e:
+ time.sleep(0.5)
+
+ data = save_bz2(sock, 'results.tar.bz2' )
+ print( "[INFO ] All done" )
+
+
+if __name__ == '__main__':
+ import argparse
+ # Argument parser.
+ description = '''Submit a job to moose server.'''
+ parser = argparse.ArgumentParser(description=description)
+ parser.add_argument('path', metavar='path'
+ , help = 'File or directory to execute on server.'
+ )
+ parser.add_argument('--main', '-m', action = 'append'
+ , required = False, default = []
+ , help = 'In case of multiple files, scripts to execute'
+ ' on the server, e.g. -m file1.py -m file2.py.'
+ ' If not given, server will try to guess the best option.'
+ )
+ parser.add_argument('--server', '-s'
+ , required = False, type=str, default='localhost:31417'
+ , help = 'IP address and PORT number of moose server e.g.'
+ ' 172.16.1.2:31416'
+ )
+ class Args: pass
+ args = Args()
+ parser.parse_args(namespace=args)
+ main(args)
diff --git a/moose-core/shell/Shell.cpp b/moose-core/shell/Shell.cpp
index aa7cc9831ef67209ae02853fddc9b5a5eba4ab87..1043f19d8b64af5eb157414ed15dd49b4a750603 100644
--- a/moose-core/shell/Shell.cpp
+++ b/moose-core/shell/Shell.cpp
@@ -9,6 +9,7 @@
#include <string>
#include <algorithm>
+#include <chrono>
#include "../basecode/header.h"
#include "../basecode/global.h"
@@ -20,10 +21,12 @@
#include "../msg/OneToOneMsg.h"
#include "../msg/OneToAllMsg.h"
#include "../msg/SparseMsg.h"
+#include "../builtins/SocketStreamer.h"
#include "Shell.h"
#include "Wildcard.h"
+
// Want to separate out this search path into the Makefile options
#include "../scheduling/Clock.h"
@@ -42,6 +45,7 @@ bool Shell::doReinit_( 0 );
bool Shell::isParserIdle_( 0 );
double Shell::runtime_( 0.0 );
+
const Cinfo* Shell::initCinfo()
{
@@ -62,18 +66,19 @@ const Cinfo* Shell::initCinfo()
////////////////////////////////////////////////////////////////
// Dest Finfos: Functions handled by Shell
////////////////////////////////////////////////////////////////
- static DestFinfo handleUseClock( "useClock",
- "Deals with assignment of path to a given clock."
- " Arguments: path, field, tick number. ",
- new EpFunc4< Shell, string, string, unsigned int, unsigned int >(
- &Shell::handleUseClock )
+ static DestFinfo handleUseClock( "useClock"
+ , "Deals with assignment of path to a given clock."
+ " Arguments: path, field, tick number. "
+ , new EpFunc4< Shell, string, string, unsigned int, unsigned int >(&Shell::handleUseClock )
);
- static DestFinfo handleCreate( "create",
- "create( class, parent, newElm, name, numData, isGlobal )",
- new EpFunc6< Shell, string, ObjId, Id, string, NodeBalance, unsigned int >( &Shell::handleCreate ) );
- static DestFinfo handleDelete( "delete",
- "When applied to a regular object, this function operates "
+ static DestFinfo handleCreate( "create"
+ , "create( class, parent, newElm, name, numData, isGlobal )"
+ , new EpFunc6<Shell, string, ObjId, Id, string, NodeBalance, unsigned int>(&Shell::handleCreate)
+ );
+
+ static DestFinfo handleDelete( "delete"
+ , "When applied to a regular object, this function operates "
"on the Id (element) specified by the ObjId argument. "
"The function deletes the entire object "
"array on this Id, including all dataEntries on it,"
@@ -81,41 +86,48 @@ const Cinfo* Shell::initCinfo()
"is ignored, and all dataEntries are destroyed. \n"
"When applied to a message: Destroys only that one specific "
"message identified by the full ObjId. \n"
- "Args: ObjId\n",
- new EpFunc1< Shell, ObjId >( & Shell::destroy ) );
-
- static DestFinfo handleAddMsg( "addMsg",
- "Makes a msg. Arguments are:"
- " msgtype, src object, src field, dest object, dest field",
- new EpFunc6< Shell, string, ObjId, string, ObjId, string, unsigned int >
- ( & Shell::handleAddMsg ) );
- static DestFinfo handleQuit( "quit",
- "Stops simulation running and quits the simulator",
- new OpFunc0< Shell >( & Shell::handleQuit ) );
- static DestFinfo handleMove( "move",
- "handleMove( Id orig, Id newParent ): "
- "moves an Element to a new parent",
- new EpFunc2< Shell, Id, ObjId >( & Shell::handleMove ) );
- static DestFinfo handleCopy( "copy",
- "handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): "
+ "Args: ObjId\n"
+ , new EpFunc1< Shell, ObjId >( & Shell::destroy )
+ );
+
+ static DestFinfo handleAddMsg( "addMsg"
+ , "Makes a msg. Arguments are:"
+ " msgtype, src object, src field, dest object, dest field"
+ , new EpFunc6< Shell, string, ObjId, string, ObjId, string, unsigned int >(&Shell::handleAddMsg)
+ );
+
+ static DestFinfo handleQuit( "quit"
+ , "Stops simulation running and quits the simulator"
+ , new OpFunc0< Shell >( & Shell::handleQuit )
+ );
+ static DestFinfo handleMove( "move"
+ , "handleMove( Id orig, Id newParent ): "
+ "moves an Element to a new parent"
+ , new EpFunc2<Shell, Id, ObjId>( & Shell::handleMove )
+ );
+
+ static DestFinfo handleCopy( "copy"
+ , "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.",
- new EpFunc5< Shell, vector< ObjId >, string, unsigned int, bool, bool >(
- & Shell::handleCopy ) );
+ " If the flag copyExtMsgs is true, then all msgs going out are also copied."
+ , new EpFunc5< Shell, vector< ObjId >, string, unsigned int, bool, bool >(
+ & Shell::handleCopy )
+ );
- static DestFinfo setclock( "setclock",
- "Assigns clock ticks. Args: tick#, dt",
- new OpFunc2< Shell, unsigned int, double >( & Shell::doSetClock ) );
+ static DestFinfo setclock( "setclock"
+ , "Assigns clock ticks. Args: tick#, dt"
+ , new OpFunc2< Shell, unsigned int, double >( & Shell::doSetClock )
+ );
static Finfo* shellFinfos[] =
{
&setclock,
-////////////////////////////////////////////////////////////////
-// Shared msg
-////////////////////////////////////////////////////////////////
+ ////////////////////////////////////////////////////////////////
+ // Shared msg
+ ////////////////////////////////////////////////////////////////
// &master,
// &worker,
&handleCreate,
@@ -220,7 +232,7 @@ Id Shell::doCreate( string type, ObjId parent, string name,
{
stringstream ss;
ss << "Object with same path already present : " << parent.path()
- << "/" << name;
+ << "/" << name;
moose::showWarn( ss.str() );
return Id();
}
@@ -358,17 +370,14 @@ bool isDoingReinit()
{
static Id clockId( 1 );
assert( clockId.element() != 0 );
-
- return ( reinterpret_cast< const Clock* >(
- clockId.eref().data() ) )->isDoingReinit();
+ return (reinterpret_cast<const Clock*>(clockId.eref().data()))->isDoingReinit();
}
+
void Shell::doReinit( )
{
-
Id clockId( 1 );
SetGet0::set( clockId, "reinit" );
-
}
void Shell::doStop( )
@@ -1028,7 +1037,7 @@ void Shell::cleanSimulation()
if ( i->value() > 4 ) /* These are created by users */
{
LOG( moose::debug
- , "Shell::cleanSimulation: deleted cruft at " <<
+ , "Shell::cleanSimulation: deleted cruft at " <<
i->value() << ": " << i->path());
s->doDelete( *i );
}
diff --git a/moose-core/shell/Shell.h b/moose-core/shell/Shell.h
index 40c36b3c36c71aaa289317f2bf86f84513bb8d43..1853a1ee640b989310af5ea245c2592462b1e8d0 100644
--- a/moose-core/shell/Shell.h
+++ b/moose-core/shell/Shell.h
@@ -44,41 +44,6 @@ public:
Shell();
~Shell();
-#ifdef CYMOOSE
-
- /**
- * @brief Initialize shell.
- *
- * @return Pointer to shell.
- *
- * This function initialize shell and returns a pointer to it.
- * This function must create a fully functional shell which can
- * be used by cython interface.
- */
- Shell* initShell();
-
-
- /**
- * @brief A thin wrapper around doCreate function. Used in
- * cython interface.
- *
- * @param type Type of Moose-element to be created e.g. Table,
- * Compartment, etc.
- * @param parent Parent element under which this element is
- * being created.
- * @param name Name of the element. String.
- * @param numData
- * @param nodePolicy
- * @param preferredNode
- *
- * @return Id of the element.
- */
- Id create( string type, string name, unsigned int numData,
- NodePolicy nodePolicy = MooseBlockBalance,
- unsigned int preferredNode = 1 );
-
-
-#endif /* ----- CYMOOSE ----- */
///////////////////////////////////////////////////////////
// Field functions
///////////////////////////////////////////////////////////
@@ -102,6 +67,8 @@ public:
*/
bool isRunning() const;
+ void setupSocketStreamer(const string host, const int port );
+
///////////////////////////////////////////////////////////
// Parser functions
///////////////////////////////////////////////////////////
diff --git a/moose-core/shell/Wildcard.cpp b/moose-core/shell/Wildcard.cpp
index 9031759ac6484d1fd8c76956f9726f88f361ed86..abfb4f7de5fe6b55bc435b76217871e014a09b2c 100644
--- a/moose-core/shell/Wildcard.cpp
+++ b/moose-core/shell/Wildcard.cpp
@@ -151,9 +151,10 @@ static void myUnique(vector<ObjId>& ret)
ret.resize(j);
}
-int wildcardFind(const string& path, vector<ObjId>& ret)
+int wildcardFind(const string& path, vector<ObjId>& ret, bool clear)
{
- ret.resize( 0 );
+ if(clear)
+ ret.resize( 0 );
simpleWildcardFind( path, ret );
myUnique( ret );
return ret.size();
diff --git a/moose-core/shell/Wildcard.h b/moose-core/shell/Wildcard.h
index 912b37086b5a1b0e6b61409c0fe38cbd97e37875..1fd975789f25b6d1abeaac753134d99b0c2e4f3d 100644
--- a/moose-core/shell/Wildcard.h
+++ b/moose-core/shell/Wildcard.h
@@ -57,8 +57,10 @@ int simpleWildcardFind( const string& path, vector<ObjId>& ret);
* wildcardFind returns the number of Ids found.
* This behaves the same as simpleWildcardFind, except that it eliminates
* non-unique entries, and in the process will scramble the ordering.
+ *
+ * If clear=true, then reset the ret to 0 size.
*/
-int wildcardFind(const string& n, vector<ObjId>& ret);
+int wildcardFind(const string& n, vector<ObjId>& ret, bool clear = true);
/**
* Recursive function to compare all descendants and cram matches into ret.
diff --git a/moose-core/tests/python/models.py b/moose-core/tests/python/models.py
new file mode 100644
index 0000000000000000000000000000000000000000..3a5443f559e1ee361a83f094b9a7fe5cfa37b6f6
--- /dev/null
+++ b/moose-core/tests/python/models.py
@@ -0,0 +1,26 @@
+# Library of simple models.
+import moose
+
+def simple_model_a():
+ compt = moose.CubeMesh( '/compt' )
+ r = moose.Reac( '/compt/r' )
+ a = moose.Pool( '/compt/a' )
+ a.concInit = 1
+ b = moose.Pool( '/compt/b' )
+ b.concInit = 2
+ c = moose.Pool( '/compt/c' )
+ c.concInit = 0.5
+ moose.connect( r, 'sub', a, 'reac' )
+ moose.connect( r, 'prd', b, 'reac' )
+ moose.connect( r, 'prd', c, 'reac' )
+ r.Kf = 0.1
+ r.Kb = 0.01
+
+ tabA = moose.Table2( '/compt/a/tab' )
+ tabB = moose.Table2( '/compt/tabB' )
+ tabC = moose.Table2( '/compt/tabB/tabC' )
+ print(tabA, tabB, tabC)
+ moose.connect( tabA, 'requestOut', a, 'getConc' )
+ moose.connect( tabB, 'requestOut', b, 'getConc' )
+ moose.connect( tabC, 'requestOut', c, 'getConc' )
+ return [tabA, tabB, tabC]
diff --git a/moose-core/tests/python/test_moose_attribs.py b/moose-core/tests/python/test_moose_attribs.py
index 4d3d97702aa3ffc97c6b72948b82c6d02914cd81..b10a2b30a4be8e81e56307da6cffcbaa6f793f07 100644
--- a/moose-core/tests/python/test_moose_attribs.py
+++ b/moose-core/tests/python/test_moose_attribs.py
@@ -44,7 +44,7 @@ attribs = ['AdExIF', 'AdThreshIF', 'Adaptor', 'Annotator', 'Arith', 'BufPool',
'element', 'exists', 'finfotypes', 'fixXreacs', 'genesis', 'getCwe',
'getField', 'getFieldDict', 'getFieldNames', 'getfielddoc',
'getmoosedoc', 'isRunning',
- 'known_types', 'le', 'listmsg', 'loadModel', 'melement',
+ 'known_types', 'le', 'listmsg', 'loadModelInternal', 'melement',
'mergeChemModel', 'moose',
'mooseAddChemSolver', 'mooseDeleteChemSolver', 'mooseReadNML2',
'mooseReadSBML', 'mooseWriteKkit', 'mooseWriteNML2', 'mooseWriteSBML',
@@ -52,7 +52,7 @@ attribs = ['AdExIF', 'AdThreshIF', 'Adaptor', 'Annotator', 'Arith', 'BufPool',
'nml2Import_', 'pager', 'print_utils',
'pwe', 'pydoc', 'rand', 'reinit',
'seed', 'sequence_types', 'setClock', 'setCwe', 'showfield',
- 'showfields', 'showmsg', 'splitext', 'start', 'stop', 'syncDataHandler',
+ 'showfields', 'showmsg', 'start', 'stop', 'syncDataHandler',
'test', 'testSched', 'toUnicode', 'useClock', 'utils', 'vec', 'version',
'warnings', 'wildcardFind']
diff --git a/moose-core/tests/python/test_socket_streamer_tcp.py b/moose-core/tests/python/test_socket_streamer_tcp.py
new file mode 100644
index 0000000000000000000000000000000000000000..497b66fb0412df6a1e454dca10ed19775bb1a59f
--- /dev/null
+++ b/moose-core/tests/python/test_socket_streamer_tcp.py
@@ -0,0 +1,182 @@
+# -*- coding: utf-8 -*-
+"""test_socket_streamer.py:
+
+ MOOSE must create a socket server on PORT 31616 (default)
+ or setup moose.SocketStreamer port to appropriate port number.
+
+ Client can read data from this socket.
+"""
+
+from __future__ import print_function
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2016, Dilawar Singh"
+__credits__ = ["NCBS Bangalore"]
+__license__ = "GNU GPL"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+import os
+import sys
+sys.path.append( os.path.dirname(__file__))
+import time
+import socket
+import numpy as np
+import threading
+import moose
+import models
+import json
+from collections import defaultdict
+
+finish_all_ = False
+
+print( '[INFO] Using moose form %s' % moose.__file__ )
+
+def get_msg(s, n=1024):
+ d = s.recv( n, socket.MSG_WAITALL)
+ while len(d) < n:
+ d += s.recv(n-len(d), socket.MSG_WAITALL)
+ return d
+
+def socket_client(host='127.0.0.1', port = 31416):
+ # This function waits for socket to be available.
+ global finish_all_
+ s = socket.socket( socket.AF_INET, socket.SOCK_STREAM )
+ while 1:
+ if finish_all_:
+ print( '[INFO] MOOSE is done before I could connect' )
+ break
+ # print('Py: Trying to connect to %s, %s' % (host, port))
+ # print( end = '.' )
+ try:
+ s.connect( ('', port) )
+ break
+ except Exception as e:
+ continue
+ print(e, end = 'x')
+ sys.stdout.flush()
+ pass
+
+ print( 'Connected' )
+ if not finish_all_:
+ print( 'Py: Connected with socket.' )
+
+ # This is client reponsibility to read the data.
+ s.settimeout(0.1)
+ data = b''
+ while not finish_all_:
+ try:
+ data += get_msg(s)
+ except socket.timeout as e:
+ print( e, end = ' ' )
+
+ s.close()
+ assert data, "No data streamed"
+ print( 'recieved data:\n', data )
+ res = defaultdict(list)
+ for x in data.split(b'\n'):
+ if not x.strip():
+ continue
+ d = json.loads(x)
+ for k, v in d.items():
+ res[k] += v
+
+ expected = {u'/compt/tabB/tabC': ([25.,1.07754388], [14.71960144, 0.16830373])
+ , u'/compt/a/tab': ([25., 0.42467006], [14.71960144, 0.16766705])
+ , u'/compt/tabB': ([25., 2.57797725], [14.71960144, 0.16842971])
+ }
+ nd = {}
+ for k in res:
+ v = res[k]
+ nd[k] = (np.mean(v, axis=0), np.std(v, axis=0))
+ assert np.isclose(expected[k], nd[k]).all(), \
+ "Exptected %s, got %s" % (str(expected[k]), str(nd[k]))
+
+def sanity_test( ):
+ a = moose.Table( '/t1' )
+ b = moose.Table( '/t1/t1' )
+ c = moose.Table( '/t1/t1/t1' )
+ st = moose.SocketStreamer( '/s' )
+ st.addTable( a )
+ assert( st.numTables == 1 )
+ st.addTable( b )
+ assert( st.numTables == 2 )
+ st.addTable( c )
+ assert( st.numTables == 3 )
+ st.addTable( c )
+ assert( st.numTables == 3 )
+ st.addTable( c )
+ assert( st.numTables == 3 )
+
+ st.removeTable( c )
+ assert( st.numTables == 2 )
+ st.removeTable( c )
+ assert( st.numTables == 2 )
+ st.removeTable( a )
+ assert( st.numTables == 1 )
+ st.removeTable( b )
+ assert( st.numTables == 0 )
+ st.removeTable( b )
+ assert( st.numTables == 0 )
+ print( 'Sanity test passed' )
+
+ st.addTables( [a, b, c ])
+ assert st.numTables == 3
+ st.removeTables( [a, a, c] )
+ assert st.numTables == 1
+ moose.delete( '/t1' )
+ moose.delete( '/s' )
+
+def test():
+ global finish_all_
+ os.environ['MOOSE_STREAMER_ADDRESS'] = 'http://127.0.0.1:31416'
+ client = threading.Thread(target=socket_client, args=())
+ # client.daemon = True
+ client.start()
+ print( '[INFO] Socket client is running now' )
+ tables = models.simple_model_a()
+ time.sleep(0.1)
+ moose.reinit()
+ moose.start(50)
+ print( 'MOOSE is done' )
+
+ # sleep for some time so data can be read.
+ time.sleep(1)
+ finish_all_ = True
+ client.join()
+ print( 'Test 1 passed' )
+
+def test_without_env():
+ global finish_all_
+ os.environ['MOOSE_STREAMER_ADDRESS'] = ''
+ client = threading.Thread(target=socket_client, args=())
+ #client.daemon = True
+ client.start()
+ print( '[INFO] Socket client is running now' )
+ tables = create_model()
+ # Now create a streamer and use it to write to a stream
+ st = moose.SocketStreamer( '/compt/streamer' )
+ st.address = 'http://127.0.0.1:31416'
+ assert st.port == 31416, "Got %s expected %s" % (st.port, expected)
+ st.addTable(tables[0])
+ st.addTables(tables[1:])
+ assert st.numTables == 3
+ # Give some time for socket client to make connection.
+ moose.reinit()
+ moose.start(50)
+ time.sleep(1)
+ print( 'MOOSE is done' )
+ # sleep for some time so data can be read.
+ finish_all_ = True
+ client.join()
+ print( 'Test 2 passed' )
+
+def main( ):
+ test( )
+ # test_without_env()
+ print( '[INFO] All tests passed' )
+
+if __name__ == '__main__':
+ main()
diff --git a/moose-core/tests/python/test_socket_streamer_uds.py b/moose-core/tests/python/test_socket_streamer_uds.py
new file mode 100644
index 0000000000000000000000000000000000000000..542c3a46b212cb98f8218816a66bd31afecb2beb
--- /dev/null
+++ b/moose-core/tests/python/test_socket_streamer_uds.py
@@ -0,0 +1,128 @@
+# -*- coding: utf-8 -*-
+"""test_socket_streamer.py:
+
+ MOOSE must create a socket server on PORT 31616 (default)
+ or setup moose.SocketStreamer port to appropriate port number.
+
+ Client can read data from this socket.
+"""
+
+from __future__ import print_function
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2016, Dilawar Singh"
+__credits__ = ["NCBS Bangalore"]
+__license__ = "GNU GPL"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+import os
+import sys
+sys.path.append(os.path.dirname(__file__))
+import time
+import socket
+import numpy as np
+import threading
+import moose
+import json
+import models
+from collections import defaultdict
+
+finish_all_ = False
+
+print( '[INFO] Using moose form %s' % moose.__file__ )
+
+sockFile_ = '/tmp/MOOSE'
+
+def get_msg(s, n=1024):
+ d = s.recv(n)
+ while(len(d) < n):
+ d1 = s.recv(n-len(d))
+ d += d1
+ return d
+
+def socket_client( ):
+ # This function waits for socket to be available.
+ global finish_all_
+ global sockFile_
+ s = socket.socket( socket.AF_UNIX, socket.SOCK_STREAM )
+ address = sockFile_
+ while 1:
+ if finish_all_:
+ print( '[INFO] MOOSE is done before I could connect' )
+ break
+ # print('Py: Trying to connect to %s, %s' % (host, port))
+ # print( end = '.' )
+ try:
+ s.connect( address )
+ break
+ except Exception as e:
+ pass
+
+ if not finish_all_:
+ print( 'Py: Connected with socket.' )
+
+ # This is client reponsibility to read the data.
+ data = b''
+ s.settimeout(1)
+ while not finish_all_:
+ try:
+ d = get_msg(s, 1024)
+ data += d
+ except socket.timeout as e:
+ pass
+ s.close()
+
+ assert data, "No data streamed"
+ res = defaultdict(list)
+ for x in data.split(b'\n'):
+ if not x.strip():
+ continue
+ x = x.decode( 'utf8' )
+ try:
+ d = json.loads(x)
+ except Exception as e:
+ print( data )
+ raise e
+ for k, v in d.items():
+ res[k] += v
+
+ expected = {u'/compt/tabB/tabC': ([25.,1.07754388], [14.71960144, 0.16830373])
+ , u'/compt/a/tab': ([25., 0.42467006], [14.71960144, 0.16766705])
+ , u'/compt/tabB': ([25., 2.57797725], [14.71960144, 0.16842971])
+ }
+ nd = {}
+ for k in res:
+ v = res[k]
+ nd[k] = (np.mean(v, axis=0), np.std(v, axis=0))
+ assert np.isclose(expected[k], nd[k]).all(), \
+ "Exptected %s, got %s" % (str(expected[k]), str(nd[k]))
+
+def test():
+ global finish_all_
+ client = threading.Thread(target=socket_client, args=())
+ #client.daemon = True
+ client.start()
+ print( '[INFO] Socket client is running now' )
+ tables = models.simple_model_a()
+ # Now create a streamer and use it to write to a stream
+ os.environ['MOOSE_STREAMER_ADDRESS'] = 'file:///tmp/moose'
+
+ # Give some time for socket client to make connection.
+ moose.reinit()
+ moose.start(50)
+ time.sleep(0.1)
+ finish_all_ = True
+ print( 'MOOSE is done' )
+ # sleep for some time so data can be read.
+ client.join()
+ print( 'Test 2 passed' )
+
+def main( ):
+ test()
+ print( '[INFO] All tests passed' )
+
+if __name__ == '__main__':
+ main()
diff --git a/moose-core/utility/setupenv.cpp b/moose-core/utility/setupenv.cpp
index 3d8b32714927c705d733c3f49aca4a5414323368..422d3471d234fe051b1fcbb6d7c8f8f744ad176c 100644
--- a/moose-core/utility/setupenv.cpp
+++ b/moose-core/utility/setupenv.cpp
@@ -38,6 +38,7 @@ using namespace std;
extern unsigned getNumCores();
namespace moose {
+
const map<string, string>& getArgMap()
{
static map<string, string> argmap;
@@ -105,6 +106,23 @@ namespace moose {
return argmap;
}
+ /* --------------------------------------------------------------------------*/
+ /**
+ * @Synopsis Get environment valus.
+ *
+ * @Param env Name of the environment variable.
+ *
+ * @Returns value of environment if set, empty string otherwise.
+ */
+ /* ----------------------------------------------------------------------------*/
+ string getEnv( const string& env )
+ {
+ const char* pEnv = std::getenv( env.c_str() );
+ if( pEnv )
+ return string(pEnv);
+ return "";
+ }
+
}
diff --git a/moose-core/utility/strutil.cpp b/moose-core/utility/strutil.cpp
index da5ee41f3516092a294567923297289fd92f8c5e..95b094509ff0467ccbfd89ce4a21cf35b3718295 100644
--- a/moose-core/utility/strutil.cpp
+++ b/moose-core/utility/strutil.cpp
@@ -5,7 +5,9 @@
* E-mail: ray.subhasis@gmail.com
* Created: 2007-09-25 12:12:10
********************************************************************/
+
#include <string>
+#include <sstream>
#include <iostream>
#include <vector>
#include "strutil.h"
diff --git a/moose-core/utility/strutil.h b/moose-core/utility/strutil.h
index a5b1760b2c278fe7abde7aeaf52eab27e59bb38a..4d95c1419f2ce8fd197dc6ef0c292809f7c4be68 100644
--- a/moose-core/utility/strutil.h
+++ b/moose-core/utility/strutil.h
@@ -48,10 +48,33 @@ namespace moose
*/
int strncasecmp( const std::string& a, const std::string& b, size_t n);
- /**
- * Generate random string of given length.
- */
- std::string random_string( const unsigned size );
+ /**
+ * Generate random string of given length.
+ */
+ std::string random_string( const unsigned size );
+
+
+ /* --------------------------------------------------------------------------*/
+ /**
+ * @Synopsis Converts a vector to string.
+ *
+ * @Param vec
+ *
+ * @Returns
+ */
+ /* ----------------------------------------------------------------------------*/
+ template<typename T=double>
+ std::string vectorToCSV( const std::vector<T>& vec)
+ {
+ std::stringstream ss;
+ for(size_t i = 0; i < vec.size(); i++)
+ ss << vec[i] << ',';
+ auto res = ss.str();
+ if( ',' == res.back())
+ res.pop_back();
+ return res;
+ }
+
}
#endif //_STRINGUTIL_H
diff --git a/moose-core/utility/utility.h b/moose-core/utility/utility.h
index 4d5510186b9b682233feca04b3487979728cee7c..ee0e88d7f1743de877bc0d09981b4d6c03c2e61c 100644
--- a/moose-core/utility/utility.h
+++ b/moose-core/utility/utility.h
@@ -20,7 +20,10 @@ namespace moose
char shortType(std::string type);
char innerType(char typecode);
char shortFinfo(std::string ftype);
+
+ // In setuptevn.cpp
const map<std::string, std::string>& getArgMap();
+ string getEnv( const string& env);
/**
* @brief Givem path of MOOSE element, return its name. It's behaviour is